Mercurial > repos > iuc > sleuth
annotate sleuth.R @ 0:5f1cb4c28d73 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
author | iuc |
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date | Thu, 01 Jun 2023 07:56:00 +0000 |
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children | d3e447dd52c8 |
rev | line source |
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0
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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1 library(sleuth, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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2 quietly = TRUE, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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3 warn.conflicts = FALSE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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4 library(annotables, quietly = TRUE, warn.conflicts = FALSE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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5 library(argparse, quietly = TRUE, warn.conflicts = FALSE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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6 library(tidyverse) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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7 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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8 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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9 # setup R error handling to go to stderr |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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10 options( |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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11 show.error.messages = FALSE, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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12 error = function() { |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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13 cat(geterrmessage(), file = stderr()) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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14 q("no", 1, FALSE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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15 } |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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16 ) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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17 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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18 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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19 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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20 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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21 ################################################################################ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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22 ### Input Processing |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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23 ################################################################################ |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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24 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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25 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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26 # Collect arguments from command line |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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27 parser <- ArgumentParser(description = "Sleuth R script") |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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28 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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29 parser$add_argument("--factorLevel", action = "append", required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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30 parser$add_argument("--factorLevel_counts", |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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31 action = "append", |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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32 required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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33 parser$add_argument("--factorLevel_n", action = "append", required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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34 parser$add_argument("--cores", type = "integer", required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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35 parser$add_argument("--normalize", action = "store_true", required = FALSE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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36 parser$add_argument("--nbins", type = "integer", required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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37 parser$add_argument("--lwr", type = "numeric", required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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38 parser$add_argument("--upr", type = "numeric", required = TRUE) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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39 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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40 args <- parser$parse_args() |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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41 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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42 all_files <- args$factorLevel_counts |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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43 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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44 conditions <- c() |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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45 for (x in seq_along(args$factorLevel)) { |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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46 temp <- append(conditions, rep(args$factorLevel[[x]])) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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47 conditions <- temp |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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48 } |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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49 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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50 sample_names <- all_files %>% |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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51 str_replace(pattern = "\\.tab", "") |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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52 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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53 design <- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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54 data.frame(list( |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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55 sample = sample_names, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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56 condition = conditions, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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57 path = all_files |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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58 )) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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59 so <- sleuth_prep(design, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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60 cores = args$cores, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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61 normalize = args$normalize) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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62 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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63 so <- sleuth_fit( |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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64 so, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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65 ~ condition, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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66 "full", |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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67 n_bins = args$nbins, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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68 lwr = args$lwr, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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69 upr = args$upr |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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70 ) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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71 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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72 so <- sleuth_fit( |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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73 so, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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74 ~ 1, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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75 "reduced", |
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76 n_bins = args$nbins, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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77 lwr = args$lwr, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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78 upr = args$upr |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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79 ) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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80 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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81 so <- sleuth_lrt(so, "reduced", "full") |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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82 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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83 sleuth_table <- |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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84 sleuth_results(so, "reduced:full", "lrt", show_all = FALSE) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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85 |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
iuc
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86 write.table( |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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87 sleuth_table, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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88 file = "sleuth_table.tab", |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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89 quote = FALSE, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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90 sep = "\t", |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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91 col.names = TRUE, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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92 row.names = FALSE |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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93 ) |
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94 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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95 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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96 outputFile <- file.path(getwd(), "pca_plot.pdf") |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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97 pdf(file = outputFile, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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98 height = 6, |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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99 width = 9) |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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100 plot_pca(so, color_by = "condition") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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101 dev.off() |
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102 |
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103 outputFile <- file.path(getwd(), "group_density.pdf") |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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104 pdf(file = outputFile, |
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105 height = 6, |
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106 width = 9) |
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107 plot_group_density( |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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108 so, |
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109 use_filtered = TRUE, |
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110 units = "est_counts", |
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111 trans = "log", |
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112 grouping = setdiff(colnames(so$sample_to_covariates), |
5f1cb4c28d73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth commit 6b943159b4d68812dc6911309f23d54ec659282f
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113 "sample"), |
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114 offset = 1 |
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115 ) |
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116 dev.off() |