Mercurial > repos > iuc > limma_voom
annotate test-data/out_rscript.txt @ 4:a61a6e62e91f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
author | iuc |
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date | Sun, 29 Apr 2018 17:36:42 -0400 |
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children | d8a55b5f0de0 |
rev | line source |
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4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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1 # This tool takes in a matrix of feature counts as well as gene annotations and |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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2 # outputs a table of top expressions as well as various plots for differential |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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3 # expression analysis |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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4 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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5 # ARGS: htmlPath", "R", 1, "character" -Path to html file linking to other outputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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6 # outPath", "o", 1, "character" -Path to folder to write all output to |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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7 # filesPath", "j", 2, "character" -JSON list object if multiple files input |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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8 # matrixPath", "m", 2, "character" -Path to count matrix |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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9 # factFile", "f", 2, "character" -Path to factor information file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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10 # factInput", "i", 2, "character" -String containing factors if manually input |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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11 # annoPath", "a", 2, "character" -Path to input containing gene annotations |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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12 # contrastData", "C", 1, "character" -String containing contrasts of interest |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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13 # cpmReq", "c", 2, "double" -Float specifying cpm requirement |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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14 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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15 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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16 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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17 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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18 # lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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19 # pValReq", "p", 1, "double" -Float specifying the p-value requirement |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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20 # pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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21 # normOpt", "n", 1, "character" -String specifying type of normalisation used |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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22 # robOpt", "b", 0, "logical" -String specifying if robust options should be used |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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23 # trend", "t", 1, "double" -Float for prior.count if limma-trend is used instead of voom |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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24 # weightOpt", "w", 0, "logical" -String specifying if voomWithQualityWeights should be used |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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25 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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26 # OUT: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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27 # MDS Plot |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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28 # Voom/SA plot |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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29 # MD Plot |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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30 # Expression Table |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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31 # HTML file linking to the ouputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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32 # Optional: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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33 # Normalised counts Table |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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34 # RData file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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35 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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36 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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37 # Author: Shian Su - registertonysu@gmail.com - Jan 2014 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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38 # Modified by: Maria Doyle - Jun 2017, Jan 2018 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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39 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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40 # Record starting time |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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41 timeStart <- as.character(Sys.time()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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42 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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43 # Load all required libraries |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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44 library(methods, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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45 library(statmod, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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46 library(splines, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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47 library(edgeR, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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48 library(limma, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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49 library(scales, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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50 library(getopt, quietly=TRUE, warn.conflicts=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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51 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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52 if (packageVersion("limma") < "3.20.1") { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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53 stop("Please update 'limma' to version >= 3.20.1 to run this tool") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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54 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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55 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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56 ################################################################################ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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57 ### Function Delcaration |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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58 ################################################################################ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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59 # Function to sanitise contrast equations so there are no whitespaces |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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60 # surrounding the arithmetic operators, leading or trailing whitespace |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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61 sanitiseEquation <- function(equation) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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62 equation <- gsub(" *[+] *", "+", equation) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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63 equation <- gsub(" *[-] *", "-", equation) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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64 equation <- gsub(" *[/] *", "/", equation) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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65 equation <- gsub(" *[*] *", "*", equation) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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66 equation <- gsub("^\\s+|\\s+$", "", equation) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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67 return(equation) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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68 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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69 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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70 # Function to sanitise group information |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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71 sanitiseGroups <- function(string) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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72 string <- gsub(" *[,] *", ",", string) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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73 string <- gsub("^\\s+|\\s+$", "", string) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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74 return(string) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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75 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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76 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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77 # Function to change periods to whitespace in a string |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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78 unmake.names <- function(string) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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79 string <- gsub(".", " ", string, fixed=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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80 return(string) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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81 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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82 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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83 # Generate output folder and paths |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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84 makeOut <- function(filename) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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85 return(paste0(opt$outPath, "/", filename)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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86 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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87 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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88 # Generating design information |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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89 pasteListName <- function(string) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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90 return(paste0("factors$", string)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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91 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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92 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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93 # Create cata function: default path set, default seperator empty and appending |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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94 # true by default (Ripped straight from the cat function with altered argument |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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95 # defaults) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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96 cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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97 append = TRUE) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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98 if (is.character(file)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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99 if (file == "") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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100 file <- stdout() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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101 else if (substring(file, 1L, 1L) == "|") { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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102 file <- pipe(substring(file, 2L), "w") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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103 on.exit(close(file)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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104 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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105 else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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106 file <- file(file, ifelse(append, "a", "w")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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107 on.exit(close(file)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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108 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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109 .Internal(cat(list(...), file, sep, fill, labels, append)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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110 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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111 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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112 # Function to write code for html head and title |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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113 HtmlHead <- function(title) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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114 cata("<head>\n") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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115 cata("<title>", title, "</title>\n") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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116 cata("</head>\n") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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117 } |
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118 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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119 # Function to write code for html links |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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120 HtmlLink <- function(address, label=address) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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121 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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122 } |
a61a6e62e91f
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123 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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124 # Function to write code for html images |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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125 HtmlImage <- function(source, label=source, height=600, width=600) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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126 cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height) |
a61a6e62e91f
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127 cata("\" width=\"", width, "\"/>\n") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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128 } |
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129 |
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130 # Function to write code for html list items |
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131 ListItem <- function(...) { |
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132 cata("<li>", ..., "</li>\n") |
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133 } |
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134 |
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135 TableItem <- function(...) { |
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136 cata("<td>", ..., "</td>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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137 } |
a61a6e62e91f
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138 |
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139 TableHeadItem <- function(...) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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140 cata("<th>", ..., "</th>\n") |
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141 } |
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142 |
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143 ################################################################################ |
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144 ### Input Processing |
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145 ################################################################################ |
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146 |
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147 # Collect arguments from command line |
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148 args <- commandArgs(trailingOnly=TRUE) |
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149 |
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150 # Get options, using the spec as defined by the enclosed list. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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151 # Read the options from the default: commandArgs(TRUE). |
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152 spec <- matrix(c( |
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153 "htmlPath", "R", 1, "character", |
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154 "outPath", "o", 1, "character", |
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155 "filesPath", "j", 2, "character", |
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156 "matrixPath", "m", 2, "character", |
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157 "factFile", "f", 2, "character", |
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158 "factInput", "i", 2, "character", |
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159 "annoPath", "a", 2, "character", |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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160 "contrastData", "C", 1, "character", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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161 "cpmReq", "c", 1, "double", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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162 "totReq", "y", 0, "logical", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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163 "cntReq", "z", 1, "integer", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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164 "sampleReq", "s", 1, "integer", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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165 "normCounts", "x", 0, "logical", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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166 "rdaOpt", "r", 0, "logical", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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167 "lfcReq", "l", 1, "double", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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168 "pValReq", "p", 1, "double", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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169 "pAdjOpt", "d", 1, "character", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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170 "normOpt", "n", 1, "character", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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171 "robOpt", "b", 0, "logical", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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172 "trend", "t", 1, "double", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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173 "weightOpt", "w", 0, "logical"), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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174 byrow=TRUE, ncol=4) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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175 opt <- getopt(spec) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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176 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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177 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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178 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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179 cat("A counts matrix (or a set of counts files) is required.\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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180 q(status=1) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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181 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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182 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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183 if (is.null(opt$cpmReq)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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184 filtCPM <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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185 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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186 filtCPM <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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187 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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188 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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189 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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190 filtSmpCount <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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191 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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192 filtSmpCount <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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193 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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194 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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195 if (is.null(opt$totReq)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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196 filtTotCount <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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197 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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198 filtTotCount <- TRUE |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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199 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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200 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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201 if (is.null(opt$rdaOpt)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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202 wantRda <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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203 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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204 wantRda <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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205 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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206 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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207 if (is.null(opt$annoPath)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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208 haveAnno <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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209 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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210 haveAnno <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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211 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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212 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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213 if (is.null(opt$normCounts)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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214 wantNorm <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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215 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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216 wantNorm <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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217 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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218 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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219 if (is.null(opt$robOpt)) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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220 wantRobust <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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221 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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222 wantRobust <- TRUE |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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223 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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224 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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225 if (is.null(opt$weightOpt)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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226 wantWeight <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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227 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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228 wantWeight <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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229 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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230 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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231 if (is.null(opt$trend)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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232 wantTrend <- FALSE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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233 deMethod <- "limma-voom" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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234 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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235 wantTrend <- TRUE |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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236 deMethod <- "limma-trend" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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237 priorCount <- opt$trend |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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|
238 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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239 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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240 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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241 if (!is.null(opt$filesPath)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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242 # Process the separate count files (adapted from DESeq2 wrapper) |
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243 library("rjson") |
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244 parser <- newJSONParser() |
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245 parser$addData(opt$filesPath) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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246 factorList <- parser$getObject() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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247 factors <- sapply(factorList, function(x) x[[1]]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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248 filenamesIn <- unname(unlist(factorList[[1]][[2]])) |
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249 sampleTable <- data.frame(sample=basename(filenamesIn), |
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250 filename=filenamesIn, |
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251 row.names=filenamesIn, |
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252 stringsAsFactors=FALSE) |
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253 for (factor in factorList) { |
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254 factorName <- factor[[1]] |
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255 sampleTable[[factorName]] <- character(nrow(sampleTable)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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256 lvls <- sapply(factor[[2]], function(x) names(x)) |
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257 for (i in seq_along(factor[[2]])) { |
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258 files <- factor[[2]][[i]][[1]] |
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259 sampleTable[files,factorName] <- lvls[i] |
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260 } |
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261 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls) |
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262 } |
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263 rownames(sampleTable) <- sampleTable$sample |
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264 rem <- c("sample","filename") |
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265 factors <- sampleTable[, !(names(sampleTable) %in% rem), drop=FALSE] |
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266 |
a61a6e62e91f
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267 #read in count files and create single table |
a61a6e62e91f
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268 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)}) |
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269 counts <- do.call("cbind", countfiles) |
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270 |
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271 } else { |
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272 # Process the single count matrix |
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273 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE) |
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274 row.names(counts) <- counts[, 1] |
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275 counts <- counts[ , -1] |
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276 countsRows <- nrow(counts) |
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277 |
a61a6e62e91f
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278 # Process factors |
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279 if (is.null(opt$factInput)) { |
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280 factorData <- read.table(opt$factFile, header=TRUE, sep="\t") |
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281 factors <- factorData[, -1, drop=FALSE] |
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282 } else { |
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283 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE)) |
a61a6e62e91f
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284 factorData <- list() |
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285 for (fact in factors) { |
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286 newFact <- unlist(strsplit(fact, split="::")) |
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287 factorData <- rbind(factorData, newFact) |
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288 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor. |
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289 |
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290 # Set the row names to be the name of the factor and delete first row |
a61a6e62e91f
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291 row.names(factorData) <- factorData[, 1] |
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292 factorData <- factorData[, -1] |
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293 factorData <- sapply(factorData, sanitiseGroups) |
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294 factorData <- sapply(factorData, strsplit, split=",") |
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295 factorData <- sapply(factorData, make.names) |
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296 # Transform factor data into data frame of R factor objects |
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297 factors <- data.frame(factorData) |
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298 } |
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299 } |
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300 |
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301 # if annotation file provided |
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302 if (haveAnno) { |
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303 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", stringsAsFactors=FALSE) |
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304 } |
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305 |
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306 #Create output directory |
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307 dir.create(opt$outPath, showWarnings=FALSE) |
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308 |
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309 # Split up contrasts seperated by comma into a vector then sanitise |
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310 contrastData <- unlist(strsplit(opt$contrastData, split=",")) |
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311 contrastData <- sanitiseEquation(contrastData) |
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312 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE) |
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313 |
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314 |
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315 mdsOutPdf <- makeOut("mdsplot_nonorm.pdf") |
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316 mdsOutPng <- makeOut("mdsplot_nonorm.png") |
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317 nmdsOutPdf <- makeOut("mdsplot.pdf") |
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318 nmdsOutPng <- makeOut("mdsplot.png") |
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319 maOutPdf <- character() # Initialise character vector |
a61a6e62e91f
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320 maOutPng <- character() |
a61a6e62e91f
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321 topOut <- character() |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
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322 for (i in 1:length(contrastData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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323 maOutPdf[i] <- makeOut(paste0("maplot_", contrastData[i], ".pdf")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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324 maOutPng[i] <- makeOut(paste0("maplot_", contrastData[i], ".png")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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325 topOut[i] <- makeOut(paste0(deMethod, "_", contrastData[i], ".tsv")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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|
326 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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327 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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328 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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329 sessionOut <- makeOut("session_info.txt") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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330 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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331 # Initialise data for html links and images, data frame with columns Label and |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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332 # Link |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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333 linkData <- data.frame(Label=character(), Link=character(), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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334 stringsAsFactors=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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335 imageData <- data.frame(Label=character(), Link=character(), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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336 stringsAsFactors=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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337 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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338 # Initialise vectors for storage of up/down/neutral regulated counts |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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339 upCount <- numeric() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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340 downCount <- numeric() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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341 flatCount <- numeric() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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342 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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343 ################################################################################ |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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344 ### Data Processing |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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345 ################################################################################ |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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346 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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347 # Extract counts and annotation data |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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348 print("Extracting counts") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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349 data <- list() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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350 data$counts <- counts |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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351 if (haveAnno) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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352 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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353 annoord <- geneanno[match(row.names(counts), geneanno[,1]), ] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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354 data$genes <- annoord |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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355 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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356 data$genes <- data.frame(GeneID=row.names(counts)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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|
357 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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358 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
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359 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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360 # samples. Default is no filtering |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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361 preFilterCount <- nrow(data$counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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362 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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363 if (filtCPM || filtSmpCount || filtTotCount) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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364 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
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365 if (filtTotCount) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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366 keep <- rowSums(data$counts) >= opt$cntReq |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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367 } else if (filtSmpCount) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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368 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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369 } else if (filtCPM) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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370 keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
371 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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|
372 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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373 data$counts <- data$counts[keep, ] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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374 data$genes <- data$genes[keep, , drop=FALSE] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
375 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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|
376 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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377 postFilterCount <- nrow(data$counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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378 filteredCount <- preFilterCount-postFilterCount |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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379 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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|
380 # Creating naming data |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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381 samplenames <- colnames(data$counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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382 sampleanno <- data.frame("sampleID"=samplenames, factors) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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383 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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|
384 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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385 # Generating the DGEList object "data" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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386 print("Generating DGEList object") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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387 data$samples <- sampleanno |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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388 data$samples$lib.size <- colSums(data$counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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389 data$samples$norm.factors <- 1 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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390 row.names(data$samples) <- colnames(data$counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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391 data <- new("DGEList", data) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
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|
392 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
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393 print("Generating Design") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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394 # Name rows of factors according to their sample |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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395 row.names(factors) <- names(data$counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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396 factorList <- sapply(names(factors), pasteListName) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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397 formula <- "~0" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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398 for (i in 1:length(factorList)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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399 formula <- paste(formula,factorList[i], sep="+") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
400 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
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401 formula <- formula(formula) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
402 design <- model.matrix(formula) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
403 for (i in 1:length(factorList)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
404 colnames(design) <- gsub(factorList[i], "", colnames(design), fixed=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
405 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
406 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
407 # Calculating normalising factors |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
408 print("Calculating Normalisation Factors") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
409 data <- calcNormFactors(data, method=opt$normOpt) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
410 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
411 # Generate contrasts information |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
412 print("Generating Contrasts") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
413 contrasts <- makeContrasts(contrasts=contrastData, levels=design) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
414 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
415 ################################################################################ |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
416 ### Data Output |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
417 ################################################################################ |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
418 # Plot MDS |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
419 print("Generating MDS plot") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
420 labels <- names(counts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
421 png(mdsOutPng, width=600, height=600) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
422 # Currently only using a single factor |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
423 plotMDS(data, labels=labels, col=as.numeric(factors[, 1]), cex=0.8, main="MDS Plot (unnormalised)") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
424 imageData[1, ] <- c("MDS Plot (unnormalised)", "mdsplot_nonorm.png") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
425 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
426 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
427 pdf(mdsOutPdf) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
428 plotMDS(data, labels=labels, cex=0.5) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
429 linkData[1, ] <- c("MDS Plot (unnormalised).pdf", "mdsplot_nonorm.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
430 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
431 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
432 if (wantTrend) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
433 # limma-trend approach |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
434 logCPM <- cpm(data, log=TRUE, prior.count=opt$trend) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
435 fit <- lmFit(logCPM, design) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
436 fit$genes <- data$genes |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
437 fit <- contrasts.fit(fit, contrasts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
438 if (wantRobust) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
439 fit <- eBayes(fit, trend=TRUE, robust=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
440 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
441 fit <- eBayes(fit, trend=TRUE, robust=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
442 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
443 # plot fit with plotSA |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
444 saOutPng <- makeOut("saplot.png") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
445 saOutPdf <- makeOut("saplot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
446 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
447 png(saOutPng, width=600, height=600) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
448 plotSA(fit, main="SA Plot") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
449 imgName <- "SA Plot.png" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
450 imgAddr <- "saplot.png" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
451 imageData <- rbind(imageData, c(imgName, imgAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
452 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
453 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
454 pdf(saOutPdf, width=14) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
455 plotSA(fit, main="SA Plot") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
456 linkName <- paste0("SA Plot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
457 linkAddr <- paste0("saplot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
458 linkData <- rbind(linkData, c(linkName, linkAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
459 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
460 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
461 plotData <- logCPM |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
462 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
463 # Save normalised counts (log2cpm) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
464 if (wantNorm) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
465 write.table(logCPM, file=normOut, row.names=TRUE, sep="\t", quote=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
466 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv")))) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
467 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
468 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
469 # limma-voom approach |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
470 voomOutPdf <- makeOut("voomplot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
471 voomOutPng <- makeOut("voomplot.png") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
472 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
473 if (wantWeight) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
474 # Creating voom data object and plot |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
475 png(voomOutPng, width=1000, height=600) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
476 vData <- voomWithQualityWeights(data, design=design, plot=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
477 imgName <- "Voom Plot.png" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
478 imgAddr <- "voomplot.png" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
479 imageData <- rbind(imageData, c(imgName, imgAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
480 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
481 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
482 pdf(voomOutPdf, width=14) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
483 vData <- voomWithQualityWeights(data, design=design, plot=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
484 linkName <- paste0("Voom Plot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
485 linkAddr <- paste0("voomplot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
486 linkData <- rbind(linkData, c(linkName, linkAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
487 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
488 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
489 # Generating fit data and top table with weights |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
490 wts <- vData$weights |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
491 voomFit <- lmFit(vData, design, weights=wts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
492 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
493 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
494 # Creating voom data object and plot |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
495 png(voomOutPng, width=600, height=600) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
496 vData <- voom(data, design=design, plot=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
497 imgName <- "Voom Plot" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
498 imgAddr <- "voomplot.png" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
499 imageData <- rbind(imageData, c(imgName, imgAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
500 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
501 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
502 pdf(voomOutPdf) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
503 vData <- voom(data, design=design, plot=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
504 linkName <- paste0("Voom Plot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
505 linkAddr <- paste0("voomplot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
506 linkData <- rbind(linkData, c(linkName, linkAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
507 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
508 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
509 # Generate voom fit |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
510 voomFit <- lmFit(vData, design) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
511 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
512 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
513 # Save normalised counts (log2cpm) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
514 if (wantNorm) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
515 norm_counts <- data.frame(vData$genes, vData$E) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
516 write.table(norm_counts, file=normOut, row.names=FALSE, sep="\t", quote=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
517 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv")))) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
518 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
519 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
520 # Fit linear model and estimate dispersion with eBayes |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
521 voomFit <- contrasts.fit(voomFit, contrasts) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
522 if (wantRobust) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
523 fit <- eBayes(voomFit, robust=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
524 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
525 fit <- eBayes(voomFit, robust=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
526 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
527 plotData <- vData |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
528 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
529 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
530 print("Generating normalised MDS plot") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
531 png(nmdsOutPng, width=600, height=600) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
532 # Currently only using a single factor |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
533 plotMDS(plotData, labels=labels, col=as.numeric(factors[, 1]), cex=0.8, main="MDS Plot (normalised)") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
534 imgName <- "MDS Plot (normalised)" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
535 imgAddr <- "mdsplot.png" |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
536 imageData <- rbind(imageData, c(imgName, imgAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
537 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
538 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
539 pdf(nmdsOutPdf) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
540 plotMDS(plotData, labels=labels, cex=0.5) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
541 linkName <- paste0("MDS Plot (normalised).pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
542 linkAddr <- paste0("mdsplot.pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
543 linkData <- rbind(linkData, c(linkName, linkAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
544 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
545 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
546 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
547 print("Generating DE results") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
548 status = decideTests(fit, adjust.method=opt$pAdjOpt, p.value=opt$pValReq, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
549 lfc=opt$lfcReq) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
550 sumStatus <- summary(status) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
551 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
552 for (i in 1:length(contrastData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
553 # Collect counts for differential expression |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
554 upCount[i] <- sumStatus["Up", i] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
555 downCount[i] <- sumStatus["Down", i] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
556 flatCount[i] <- sumStatus["NotSig", i] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
557 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
558 # Write top expressions table |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
559 top <- topTable(fit, coef=i, number=Inf, sort.by="P") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
560 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
561 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
562 linkName <- paste0(deMethod, "_", contrastData[i], ".tsv") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
563 linkAddr <- paste0(deMethod, "_", contrastData[i], ".tsv") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
564 linkData <- rbind(linkData, c(linkName, linkAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
565 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
566 # Plot MA (log ratios vs mean average) using limma package on weighted |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
567 pdf(maOutPdf[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
568 limma::plotMD(fit, status=status, coef=i, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
569 main=paste("MA Plot:", unmake.names(contrastData[i])), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
570 col=alpha(c("firebrick", "blue"), 0.4), values=c("1", "-1"), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
571 xlab="Average Expression", ylab="logFC") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
572 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
573 abline(h=0, col="grey", lty=2) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
574 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
575 linkName <- paste0("MA Plot_", contrastData[i], " (.pdf)") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
576 linkAddr <- paste0("maplot_", contrastData[i], ".pdf") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
577 linkData <- rbind(linkData, c(linkName, linkAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
578 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
579 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
580 png(maOutPng[i], height=600, width=600) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
581 limma::plotMD(fit, status=status, coef=i, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
582 main=paste("MA Plot:", unmake.names(contrastData[i])), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
583 col=alpha(c("firebrick", "blue"), 0.4), values=c("1", "-1"), |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
584 xlab="Average Expression", ylab="logFC") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
585 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
586 abline(h=0, col="grey", lty=2) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
587 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
588 imgName <- paste0("MA Plot_", contrastData[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
589 imgAddr <- paste0("maplot_", contrastData[i], ".png") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
590 imageData <- rbind(imageData, c(imgName, imgAddr)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
591 invisible(dev.off()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
592 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
593 sigDiff <- data.frame(Up=upCount, Flat=flatCount, Down=downCount) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
594 row.names(sigDiff) <- contrastData |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
595 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
596 # Save relevant items as rda object |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
597 if (wantRda) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
598 print("Saving RData") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
599 if (wantWeight) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
600 save(data, status, plotData, labels, factors, wts, fit, top, contrasts, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
601 design, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
602 file=rdaOut, ascii=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
603 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
604 save(data, status, plotData, labels, factors, fit, top, contrasts, design, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
605 file=rdaOut, ascii=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
606 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
607 linkData <- rbind(linkData, c((paste0(deMethod, "_analysis.RData")), (paste0(deMethod, "_analysis.RData")))) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
608 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
609 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
610 # Record session info |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
611 writeLines(capture.output(sessionInfo()), sessionOut) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
612 linkData <- rbind(linkData, c("Session Info", "session_info.txt")) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
613 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
614 # Record ending time and calculate total run time |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
615 timeEnd <- as.character(Sys.time()) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
616 timeTaken <- capture.output(round(difftime(timeEnd,timeStart), digits=3)) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
617 timeTaken <- gsub("Time difference of ", "", timeTaken, fixed=TRUE) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
618 ################################################################################ |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
619 ### HTML Generation |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
620 ################################################################################ |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
621 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
622 # Clear file |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
623 cat("", file=opt$htmlPath) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
624 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
625 cata("<html>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
626 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
627 cata("<body>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
628 cata("<h3>Limma Analysis Output:</h3>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
629 cata("Links to PDF copies of plots are in 'Plots' section below />\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
630 if (wantWeight) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
631 HtmlImage(imageData$Link[1], imageData$Label[1], width=1000) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
632 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
633 HtmlImage(imageData$Link[1], imageData$Label[1]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
634 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
635 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
636 for (i in 2:nrow(imageData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
637 HtmlImage(imageData$Link[i], imageData$Label[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
638 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
639 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
640 cata("<h4>Differential Expression Counts:</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
641 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
642 cata("<table border=\"1\" cellpadding=\"4\">\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
643 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
644 TableItem() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
645 for (i in colnames(sigDiff)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
646 TableHeadItem(i) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
647 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
648 cata("</tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
649 for (i in 1:nrow(sigDiff)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
650 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
651 TableHeadItem(unmake.names(row.names(sigDiff)[i])) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
652 for (j in 1:ncol(sigDiff)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
653 TableItem(as.character(sigDiff[i, j])) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
654 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
655 cata("</tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
656 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
657 cata("</table>") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
658 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
659 cata("<h4>Plots:</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
660 for (i in 1:nrow(linkData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
661 if (grepl(".pdf", linkData$Link[i])) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
662 HtmlLink(linkData$Link[i], linkData$Label[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
663 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
664 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
665 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
666 cata("<h4>Tables:</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
667 for (i in 1:nrow(linkData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
668 if (grepl(".tsv", linkData$Link[i])) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
669 HtmlLink(linkData$Link[i], linkData$Label[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
670 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
671 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
672 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
673 if (wantRda) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
674 cata("<h4>R Data Object:</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
675 for (i in 1:nrow(linkData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
676 if (grepl(".RData", linkData$Link[i])) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
677 HtmlLink(linkData$Link[i], linkData$Label[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
678 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
679 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
680 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
681 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
682 cata("<p>Alt-click links to download file.</p>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
683 cata("<p>Click floppy disc icon associated history item to download ") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
684 cata("all files.</p>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
685 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
686 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
687 cata("<h4>Additional Information</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
688 cata("<ul>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
689 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
690 if (filtCPM || filtSmpCount || filtTotCount) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
691 if (filtCPM) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
692 tempStr <- paste("Genes without more than", opt$cmpReq, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
693 "CPM in at least", opt$sampleReq, "samples are insignificant", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
694 "and filtered out.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
695 } else if (filtSmpCount) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
696 tempStr <- paste("Genes without more than", opt$cntReq, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
697 "counts in at least", opt$sampleReq, "samples are insignificant", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
698 "and filtered out.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
699 } else if (filtTotCount) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
700 tempStr <- paste("Genes without more than", opt$cntReq, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
701 "counts, after summing counts for all samples, are insignificant", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
702 "and filtered out.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
703 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
704 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
705 ListItem(tempStr) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
706 filterProp <- round(filteredCount/preFilterCount*100, digits=2) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
707 tempStr <- paste0(filteredCount, " of ", preFilterCount," (", filterProp, |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
708 "%) genes were filtered out for low expression.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
709 ListItem(tempStr) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
710 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
711 ListItem(opt$normOpt, " was the method used to normalise library sizes.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
712 if (wantTrend) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
713 ListItem("The limma-trend method was used.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
714 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
715 ListItem("The limma-voom method was used.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
716 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
717 if (wantWeight) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
718 ListItem("Weights were applied to samples.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
719 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
720 ListItem("Weights were not applied to samples.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
721 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
722 if (wantRobust) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
723 ListItem("eBayes was used with robust settings (robust=TRUE).") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
724 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
725 if (opt$pAdjOpt!="none") { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
726 if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
727 tempStr <- paste0("MA-Plot highlighted genes are significant at FDR ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
728 "of ", opt$pValReq," and exhibit log2-fold-change of at ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
729 "least ", opt$lfcReq, ".") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
730 ListItem(tempStr) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
731 } else if (opt$pAdjOpt=="holm") { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
732 tempStr <- paste0("MA-Plot highlighted genes are significant at adjusted ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
733 "p-value of ", opt$pValReq," by the Holm(1979) ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
734 "method, and exhibit log2-fold-change of at least ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
735 opt$lfcReq, ".") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
736 ListItem(tempStr) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
737 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
738 } else { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
739 tempStr <- paste0("MA-Plot highlighted genes are significant at p-value ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
740 "of ", opt$pValReq," and exhibit log2-fold-change of at ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
741 "least ", opt$lfcReq, ".") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
742 ListItem(tempStr) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
743 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
744 cata("</ul>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
745 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
746 cata("<h4>Summary of experimental data:</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
747 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
748 cata("<p>*CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)*</p>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
749 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
750 cata("<table border=\"1\" cellpadding=\"3\">\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
751 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
752 TableHeadItem("SampleID") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
753 TableHeadItem(names(factors)[1]," (Primary Factor)") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
754 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
755 if (ncol(factors) > 1) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
756 for (i in names(factors)[2:length(names(factors))]) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
757 TableHeadItem(i) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
758 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
759 cata("</tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
760 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
761 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
762 for (i in 1:nrow(factors)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
763 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
764 TableHeadItem(row.names(factors)[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
765 for (j in 1:ncol(factors)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
766 TableItem(as.character(unmake.names(factors[i, j]))) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
767 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
768 cata("</tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
769 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
770 cata("</table>") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
771 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
772 cit <- character() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
773 link <- character() |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
774 link[1] <- paste0("<a href=\"", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
775 "http://www.bioconductor.org/packages/release/bioc/", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
776 "vignettes/limma/inst/doc/usersguide.pdf", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
777 "\">", "limma User's Guide", "</a>.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
778 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
779 link[2] <- paste0("<a href=\"", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
780 "http://www.bioconductor.org/packages/release/bioc/", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
781 "vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
782 "\">", "edgeR User's Guide", "</a>") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
783 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
784 cit[1] <- paste("Please cite the following paper for this tool:") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
785 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
786 cit[2] <- paste("Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME,", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
787 "Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
788 "Modelling sample and observational level variability improves power ", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
789 "in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
790 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
791 cit[3] <- paste("Please cite the paper below for the limma software itself.", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
792 "Please also try to cite the appropriate methodology articles", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
793 "that describe the statistical methods implemented in limma,", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
794 "depending on which limma functions you are using. The", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
795 "methodology articles are listed in Section 2.1 of the", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
796 link[1], |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
797 "Cite no. 3 only if sample weights were used.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
798 cit[4] <- paste("Smyth GK (2005). Limma: linear models for microarray data.", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
799 "In: 'Bioinformatics and Computational Biology Solutions using", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
800 "R and Bioconductor'. R. Gentleman, V. Carey, S. doit,.", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
801 "Irizarry, W. Huber (eds), Springer, New York, pages 397-420.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
802 cit[5] <- paste("Please cite the first paper for the software itself and the", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
803 "other papers for the various original statistical methods", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
804 "implemented in edgeR. See Section 1.2 in the", link[2], |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
805 "for more detail.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
806 cit[6] <- paste("Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
807 "Bioconductor package for differential expression analysis", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
808 "of digital gene expression data. Bioinformatics 26, 139-140") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
809 cit[7] <- paste("Robinson MD and Smyth GK (2007). Moderated statistical tests", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
810 "for assessing differences in tag abundance. Bioinformatics", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
811 "23, 2881-2887") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
812 cit[8] <- paste("Robinson MD and Smyth GK (2008). Small-sample estimation of", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
813 "negative binomial dispersion, with applications to SAGE data.", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
814 "Biostatistics, 9, 321-332") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
815 cit[9] <- paste("McCarthy DJ, Chen Y and Smyth GK (2012). Differential", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
816 "expression analysis of multifactor RNA-Seq experiments with", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
817 "respect to biological variation. Nucleic Acids Research 40,", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
818 "4288-4297") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
819 cit[10] <- paste("Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
820 "precision weights unlock linear model analysis tools for", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
821 "RNA-seq read counts. Genome Biology 15, R29.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
822 cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
823 "Dobrovic A, Holloway A and Smyth GK (2006).", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
824 "Empirical array quality weights for microarray data.", |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
825 "BMC Bioinformatics 7, Article 261.") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
826 cata("<h3>Citations</h3>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
827 cata(cit[1], "\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
828 cata("<br>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
829 cata(cit[2], "\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
830 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
831 cata("<h4>limma</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
832 cata(cit[3], "\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
833 cata("<ol>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
834 ListItem(cit[4]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
835 ListItem(cit[10]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
836 ListItem(cit[11]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
837 cata("</ol>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
838 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
839 cata("<h4>edgeR</h4>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
840 cata(cit[5], "\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
841 cata("<ol>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
842 ListItem(cit[6]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
843 ListItem(cit[7]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
844 ListItem(cit[8]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
845 ListItem(cit[9]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
846 cata("</ol>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
847 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
848 cata("<p>Please report problems or suggestions to: su.s@wehi.edu.au</p>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
849 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
850 for (i in 1:nrow(linkData)) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
851 if (grepl("session_info", linkData$Link[i])) { |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
852 HtmlLink(linkData$Link[i], linkData$Label[i]) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
853 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
854 } |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
855 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
856 cata("<table border=\"0\">\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
857 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
858 TableItem("Task started at:"); TableItem(timeStart) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
859 cata("</tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
860 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
861 TableItem("Task ended at:"); TableItem(timeEnd) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
862 cata("</tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
863 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
864 TableItem("Task run time:"); TableItem(timeTaken) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
865 cata("<tr>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
866 cata("</table>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
867 |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
868 cata("</body>\n") |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
diff
changeset
|
869 cata("</html>") |