| Previous changeset 2:a330ddf43861 (2017-09-07) Next changeset 4:a61a6e62e91f (2018-04-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65 |
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modified:
limma_voom.R limma_voom.xml test-data/factorinfo.txt test-data/limma-voom_Mut-WT.tsv test-data/limma-voom_WT-Mut.tsv test-data/limma-voom_normcounts.tsv test-data/matrix.txt |
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added:
test-data/Mut1.counts test-data/Mut2.counts test-data/Mut3.counts test-data/WT1.counts test-data/WT2.counts test-data/WT3.counts test-data/limma-trend_Mut-WT.tsv test-data/limma-voom_Mut-WT_2fact.tsv test-data/limma-voom_Mut-WT_2fact_anno.tsv test-data/limma-voom_Mut-WT_anno.tsv test-data/limma-voom_WT-Mut_2fact_anno.tsv test-data/limma-voom_normcounts_anno.tsv |
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removed:
test-data/limma-voom_Mut-WTanno.tsv test-data/limma-voom_Mut-WTmultifact.tsv |
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| diff -r a330ddf43861 -r 38aab66ae5cb limma_voom.R --- a/limma_voom.R Thu Sep 07 05:27:27 2017 -0400 +++ b/limma_voom.R Wed Jan 31 12:45:42 2018 -0500 |
| [ |
| b'@@ -2,31 +2,40 @@\n # outputs a table of top expressions as well as various plots for differential\n # expression analysis\n #\n-# ARGS: 1.countPath -Path to RData input containing counts\n-# 2.annoPath -Path to input containing gene annotations\n-# 3.htmlPath -Path to html file linking to other outputs\n-# 4.outPath -Path to folder to write all output to\n-# 5.rdaOpt -String specifying if RData should be saved\n-# 6.normOpt -String specifying type of normalisation used\n-# 7.weightOpt -String specifying usage of weights\n-# 8.contrastData -String containing contrasts of interest\n-# 9.cpmReq -Float specifying cpm requirement\n-# 10.sampleReq -Integer specifying cpm requirement\n-# 11.pAdjOpt -String specifying the p-value adjustment method\n-# 12.pValReq -Float specifying the p-value requirement\n-# 13.lfcReq -Float specifying the log-fold-change requirement\n-# 14.normCounts -String specifying if normalised counts should be output\n-# 15.factPath -Path to factor information file\n-# 16.factorData -Strings containing factor names and values if manually input \n+# ARGS: htmlPath", "R", 1, "character" -Path to html file linking to other outputs\n+# outPath", "o", 1, "character" -Path to folder to write all output to\n+# filesPath", "j", 2, "character" -JSON list object if multiple files input\n+# matrixPath", "m", 2, "character" -Path to count matrix\n+# factFile", "f", 2, "character" -Path to factor information file\n+# factInput", "i", 2, "character" -String containing factors if manually input\n+# annoPath", "a", 2, "character" -Path to input containing gene annotations\n+# contrastData", "C", 1, "character" -String containing contrasts of interest\n+# cpmReq", "c", 2, "double" -Float specifying cpm requirement\n+# cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement\n+# sampleReq", "s", 2, "integer" -Integer specifying cpm requirement\n+# normCounts", "x", 0, "logical" -String specifying if normalised counts should be output\n+# rdaOpt", "r", 0, "logical" -String specifying if RData should be output\n+# lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement\n+# pValReq", "p", 1, "double" -Float specifying the p-value requirement\n+# pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method\n+# normOpt", "n", 1, "character" -String specifying type of normalisation used\n+# robOpt", "b", 0, "logical" -String specifying if robust options should be used\n+# trend", "t", 1, "double" -Float for prior.count if limma-trend is used instead of voom\n+# weightOpt", "w", 0, "logical" -String specifying if voomWithQualityWeights should be used\n #\n-# OUT: Voom Plot\n-# BCV Plot\n-# MA Plot\n+# OUT:\n+# MDS Plot\n+# Voom/SA plot\n+# MD Plot\n # Expression Table\n # HTML file linking to the ouputs\n+# Optional:\n+# Normalised counts Table\n+# RData file\n+#\n #\n # Author: Shian Su - registertonysu@gmail.com - Jan 2014\n-# Modified by: Maria Doyle - Jun 2017\n+# Modified by: Maria Doyle - Jun 2017, Jan 2018\n \n # Record starting time\n timeStart <- as.character(Sys.time())\n@@ -38,9 +47,10 @@\n library(edgeR, quietly=TRUE, warn.conflicts=FALSE)\n library(limma, quietly=TRUE, warn.conflicts=FALSE)\n library(scales, quietly=TRUE, warn.conflicts=FALSE)\n+library(getopt, quietly=TRUE, warn.conflicts=FALSE)\n \n if (packageVersion("limma") < "3.20.1") {\n- stop("Please update \'limma\' to version >= 3.20.1 to run this tool")\n+ stop("Please update \'limma\' to version >= 3.20.1 to run this tool")\n }\n \n #########################################################'..b'unt, " of ", preFilterCount," (", filterProp,\n+ "%) genes were filtered out for low expression.")\n+ ListItem(tempStr)\n }\n-if (pAdjOpt!="none") {\n- if (pAdjOpt=="BH" || pAdjOpt=="BY") {\n- tempStr <- paste0("MA-Plot highlighted genes are significant at FDR ",\n- "of ", pValReq," and exhibit log2-fold-change of at ", \n- "least ", lfcReq, ".")\n- ListItem(tempStr)\n- } else if (pAdjOpt=="holm") {\n- tempStr <- paste0("MA-Plot highlighted genes are significant at adjusted ",\n- "p-value of ", pValReq," by the Holm(1979) ",\n- "method, and exhibit log2-fold-change of at least ", \n- lfcReq, ".")\n- ListItem(tempStr)\n- }\n+ListItem(opt$normOpt, " was the method used to normalise library sizes.")\n+if (wantTrend) {\n+ ListItem("The limma-trend method was used.")\n+} else {\n+ ListItem("The limma-voom method was used.")\n+}\n+if (wantWeight) {\n+ ListItem("Weights were applied to samples.")\n } else {\n- tempStr <- paste0("MA-Plot highlighted genes are significant at p-value ",\n- "of ", pValReq," and exhibit log2-fold-change of at ", \n- "least ", lfcReq, ".")\n- ListItem(tempStr)\n+ ListItem("Weights were not applied to samples.")\n+}\n+if (wantRobust) {\n+ ListItem("eBayes was used with robust settings (robust=TRUE).")\n+}\n+if (opt$pAdjOpt!="none") {\n+ if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") {\n+ tempStr <- paste0("MA-Plot highlighted genes are significant at FDR ",\n+ "of ", opt$pValReq," and exhibit log2-fold-change of at ",\n+ "least ", opt$lfcReq, ".")\n+ ListItem(tempStr)\n+ } else if (opt$pAdjOpt=="holm") {\n+ tempStr <- paste0("MA-Plot highlighted genes are significant at adjusted ",\n+ "p-value of ", opt$pValReq," by the Holm(1979) ",\n+ "method, and exhibit log2-fold-change of at least ",\n+ opt$lfcReq, ".")\n+ ListItem(tempStr)\n+ }\n+ } else {\n+ tempStr <- paste0("MA-Plot highlighted genes are significant at p-value ",\n+ "of ", opt$pValReq," and exhibit log2-fold-change of at ",\n+ "least ", opt$lfcReq, ".")\n+ ListItem(tempStr)\n }\n cata("</ul>\\n")\n \n@@ -570,19 +753,18 @@\n TableHeadItem("SampleID")\n TableHeadItem(names(factors)[1]," (Primary Factor)")\n \n- if (ncol(factors) > 1) {\n-\n+if (ncol(factors) > 1) {\n for (i in names(factors)[2:length(names(factors))]) {\n- TableHeadItem(i)\n+ TableHeadItem(i)\n }\n cata("</tr>\\n")\n- }\n+}\n \n for (i in 1:nrow(factors)) {\n- cata("<tr>\\n")\n- TableHeadItem(row.names(factors)[i])\n- for (j in 1:ncol(factors)) {\n- TableItem(as.character(unmake.names(factors[i, j])))\n+ cata("<tr>\\n")\n+ TableHeadItem(row.names(factors)[i])\n+ for (j in 1:ncol(factors)) {\n+ TableItem(as.character(unmake.names(factors[i, j])))\n }\n cata("</tr>\\n")\n }\n@@ -638,7 +820,7 @@\n cit[10] <- paste("Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:",\n "precision weights unlock linear model analysis tools for",\n "RNA-seq read counts. Genome Biology 15, R29.")\n-cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,", \n+cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,",\n "Dobrovic A, Holloway A and Smyth GK (2006).",\n "Empirical array quality weights for microarray data.",\n "BMC Bioinformatics 7, Article 261.")\n@@ -667,9 +849,9 @@\n cata("<p>Please report problems or suggestions to: su.s@wehi.edu.au</p>\\n")\n \n for (i in 1:nrow(linkData)) {\n- if (grepl("session_info", linkData$Link[i])) {\n- HtmlLink(linkData$Link[i], linkData$Label[i])\n- }\n+ if (grepl("session_info", linkData$Link[i])) {\n+ HtmlLink(linkData$Link[i], linkData$Label[i])\n+ }\n }\n \n cata("<table border=\\"0\\">\\n")\n' |
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| diff -r a330ddf43861 -r 38aab66ae5cb limma_voom.xml --- a/limma_voom.xml Thu Sep 07 05:27:27 2017 -0400 +++ b/limma_voom.xml Wed Jan 31 12:45:42 2018 -0500 |
| [ |
| b'@@ -1,65 +1,100 @@\n-<tool id="limma_voom" name="limma-voom" version="1.2.0">\n+<tool id="limma_voom" name="limma" version="3.34.6.0">\n <description>\n- Differential expression with optional sample weights\n+ Perform differential expression with limma-voom or limma-trend\n </description>\n \n <requirements>\n- <requirement type="package" version="3.16.5">bioconductor-edger</requirement>\n- <requirement type="package" version="3.30.13">bioconductor-limma</requirement>\n- <requirement type="package" version="1.4.29">r-statmod</requirement>\n- <requirement type="package" version="0.4.1">r-scales</requirement>\n+ <requirement type="package" version="3.34.6">bioconductor-limma</requirement>\n+ <requirement type="package" version="3.20.7">bioconductor-edger</requirement>\n+ <requirement type="package" version="1.4.30">r-statmod</requirement>\n+ <requirement type="package" version="0.5.0">r-scales</requirement>\n+ <requirement type="package" version="0.2.15">r-rjson</requirement>\n+ <requirement type="package" version="1.20.0">r-getopt</requirement>\n </requirements>\n \n <version_command><![CDATA[\n- echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\\$otherPkgs\\$limma\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\\$otherPkgs\\$edgeR\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n+echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\\$otherPkgs\\$limma\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\\$otherPkgs\\$edgeR\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\\$otherPkgs\\$statmod\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\\$otherPkgs\\$scales\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\\$otherPkgs\\$rjson\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\\$otherPkgs\\$getopt\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n ]]></version_command>\n \n <command detect_errors="exit_code"><![CDATA[\n+#import json\n Rscript \'$__tool_directory__/limma_voom.R\'\n-\'$counts\'\n+\n+-R \'$outReport\'\n+-o \'$outReport.files_path\'\n+\n+#if $input.format=="files":\n+\n+ ## Adapted from DESeq2 wrapper\n+ #set $temp_factor_names = list()\n+ #for $fact in $input.rep_factor:\n+ #set $temp_factor = list()\n+ #for $g in $fact.rep_group:\n+ #set $count_files = list()\n+ #for $file in $g.countsFile:\n+ $count_files.append(str($file))\n+ #end for\n+ $temp_factor.append( {str($g.groupName): $count_files} )\n+ #end for\n+\n+ $temp_factor.reverse()\n+ $temp_factor_names.append([str($fact.factorName), $temp_factor])\n+ #end for\n+ -j \'#echo json.dumps(temp_factor_names)#\'\n+\n+#elif $input.format=="matrix":\n+ -m \'$input.counts\'\n+ #if $input.fact.ffile==\'yes\':\n+ -f \'$input.fact.finfo\'\n+ #else:\n+ -i \'${ \'|\'.join( [\'%s::%s\' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }\'\n+ #end if\n+#end if\n \n #if $anno.annoOpt==\'yes\':\n- \'$geneanno\'\n-#else:\n- None\n+ -a \'$anno.geneanno\'\n #end if\n \n-\'$outReport\'\n-\'$outReport.files_path\'\n-$rdaOption\n-$normalisationOption\n-$weightOption\n-\'$contrast\'\n+-C \'${ \',\'.join( [\'%s\' % $x.contrast for x in $rep_contrast] ) }\'\n \n-#if $filterCPM.filterLowCPM==\'yes\':\n- \'$filterCPM.cpmReq\'\n- \'$filterCPM.sampleReq\'\n-#else:\n- 0\n- 0\n+#if $f.filt.filt_select == \'yes\':\n+ #if $f.filt.cformat.format_'..b'mum log2-fold-change Required:**\n- In addition to meeting the requirement for the adjusted statistic for\n- multiple testing, the observation must have an absolute log2-fold-change\n- greater than this threshold to be considered significant, thus highlighted\n- in the MA plot.\n+**Robust Settings**\n+Option to use robust settings with eBayes, used by both liamm-voom and limma-trend. Using robust settings is usually recommended to protect against outlier genes, for more information see the `limma User\'s Guide`_. This is turned on by default.\n+\n+**Prior Count:**\n+If the limma-trend method is used, a count (`prior.count`) is added to all counts to avoid taking a log of zero, and damp down the variances of logarithms of low counts. A default of 3 is used, as recommended in the `limma User\'s Guide`_.\n+\n+**Apply Sample Weights:**\n+If the limma-voom method is used, an option is available to downweight outlier samples, such that their information is still\n+used in the statistical analysis but their impact is reduced. Use this\n+whenever significant outliers are present. The MDS plotting tool in this package\n+is useful for identifying outliers. For more information on this option see Liu et al. (2015).\n+\n \n **Outputs**\n \n-This tool outputs a table of differentially expressed genes for each contrast of interest and a HTML report with plots and additional information. Optionally you can choose to output the normalised counts table and the RData file.\n+This tool outputs\n+\n+ * a table of differentially expressed genes for each contrast of interest\n+ * a HTML report with plots and additional information\n+\n+Optionally, under **Output Options** you can choose to output\n+\n+ * a normalised counts table\n+ * an RData file\n \n -----\n \n **Citations:**\n \n-.. class:: infomark\n+Please try to cite the appropriate articles when you publish results obtained using software, as such citation is the main means by which the authors receive credit for their work.\n \n limma\n \n Please cite the paper below for the limma software itself. Please also try\n to cite the appropriate methodology articles that describe the statistical\n methods implemented in limma, depending on which limma functions you are\n-using. The methodology articles are listed in Section 2.1 of the limma\n-User\'s Guide.\n+using. The methodology articles are listed in Section 2.1 of the `limma\n+User\'s Guide`_.\n \n * Smyth GK (2005). Limma: linear models for microarray data. In:\n \'Bioinformatics and Computational Biology Solutions using R and\n@@ -435,13 +706,12 @@\n A., Holloway, A., and Smyth, G. K. (2006). Empirical array quality weights\n for microarray data. BMC Bioinformatics 7, Article 261.\n \n-.. class:: infomark\n \n edgeR\n \n Please cite the first paper for the software itself and the other papers for\n the various original statistical methods implemented in edgeR. See\n-Section 1.2 in the User\'s Guide for more detail.\n+Section 1.2 in the `edgeR User\'s Guide`_ for more detail.\n \n * Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor\n package for differential expression analysis of digital gene expression\n@@ -460,10 +730,14 @@\n \n Please report problems or suggestions to: su.s@wehi.edu.au\n \n+.. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html\n+.. _limma approach: https://www.ncbi.nlm.nih.gov/pubmed/25605792\n+.. _limma User\'s Guide: http://bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf\n .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html\n-.. _limma: http://www.bioconductor.org/packages/release/bioc/html/limma.html\n+.. _edgeR User\'s Guide: https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf\n ]]></help>\n <citations>\n+ <citation type="doi">10.1186/gb-2014-15-2-r29</citation>\n <citation type="doi">10.1093/nar/gkv412</citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/Mut1.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mut1.counts Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +GeneID Mut1 +11287 1463 +11298 1345 +11302 5 +11303 1574 +11304 361 +11305 1762 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/Mut2.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mut2.counts Wed Jan 31 12:45:42 2018 -0500 |
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| @@ -0,0 +1,7 @@ +GeneID Mut2 +11287 1441 +11298 1291 +11302 6 +11303 1519 +11304 397 +11305 1942 |
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| diff -r a330ddf43861 -r 38aab66ae5cb test-data/Mut3.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Mut3.counts Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +GeneID Mut3 +11287 1495 +11298 1346 +11302 5 +11303 1654 +11304 346 +11305 2027 |
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| diff -r a330ddf43861 -r 38aab66ae5cb test-data/WT1.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/WT1.counts Wed Jan 31 12:45:42 2018 -0500 |
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| @@ -0,0 +1,7 @@ +GeneID WT1 +11287 1699 +11298 1905 +11302 6 +11303 2099 +11304 356 +11305 2528 |
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| diff -r a330ddf43861 -r 38aab66ae5cb test-data/WT2.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/WT2.counts Wed Jan 31 12:45:42 2018 -0500 |
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| @@ -0,0 +1,7 @@ +GeneID WT2 +11287 1528 +11298 1744 +11302 8 +11303 1974 +11304 312 +11305 2438 |
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| diff -r a330ddf43861 -r 38aab66ae5cb test-data/WT3.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/WT3.counts Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +GeneID WT3 +11287 1601 +11298 1834 +11302 7 +11303 2100 +11304 337 +11305 2493 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/factorinfo.txt --- a/test-data/factorinfo.txt Thu Sep 07 05:27:27 2017 -0400 +++ b/test-data/factorinfo.txt Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ Sample Genotype Batch +Mut1 Mut b1 +Mut2 Mut b2 +Mut3 Mut b3 WT1 WT b1 WT2 WT b2 WT3 WT b3 -Mut1 Mut b1 -Mut2 Mut b2 -Mut3 Mut b3 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-trend_Mut-WT.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/limma-trend_Mut-WT.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" +"11304" 0.454006866294872 15.5347733798565 5.73783569533779 6.51380077190898e-06 3.90828046314539e-05 9.50615253604686 +"11287" 0.189211879829905 17.6560194022488 4.52571052740792 0.000138730279836171 0.000416190839508512 3.37443017677096 +"11298" -0.137906115120717 17.6760627799956 -3.28370943058883 0.00313397342215802 0.00626794684431604 -1.40612492217495 +"11303" -0.0565048762006306 17.887811868748 -1.22181580605621 0.233642901495507 0.35046435224326 -5.9848993971045 +"11305" -0.0597744562444475 18.1592280697576 -1.04836609029276 0.304913314924737 0.365895977909685 -6.17897539114193 +"11302" -0.0455235218343741 10.2501491061291 -0.373618198821297 0.711968519770644 0.711968519770644 -6.65188039014484 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_Mut-WT.tsv --- a/test-data/limma-voom_Mut-WT.tsv Thu Sep 07 05:27:27 2017 -0400 +++ b/test-data/limma-voom_Mut-WT.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ "GeneID" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" -"11304" 0.457332061341026 15.5254133001226 6.50459574633681 9.98720685006039e-07 5.99232411003624e-06 14.0741948485896 -"11287" 0.190749727701785 17.6546448244617 5.09535410066402 3.26518807654125e-05 9.79556422962375e-05 5.46773893802392 -"11298" -0.138014418336201 17.6747285193431 -3.33168485842331 0.00278753263633162 0.00557506527266324 -1.84301342041449 -"11303" -0.0558958943606989 17.886791401216 -1.30108531275576 0.205582481502297 0.254491025872973 -6.4924124057801 -"11305" -0.0606991650996633 18.1585474109909 -1.28203791127299 0.212075854894144 0.254491025872973 -6.42090197700503 -"11302" -0.0350239682204432 9.78883119065989 -0.236945963165269 0.814709535394087 0.814709535394087 -6.09497670655944 +"11304" 0.457332061341022 15.5254133001226 6.50459574633635 9.98720685007144e-07 5.99232411004286e-06 14.0741948485867 +"11287" 0.190749727701785 17.6546448244617 5.09535410066427 3.26518807653921e-05 9.79556422961764e-05 5.46773893802514 +"11298" -0.138014418336201 17.6747285193431 -3.3316848584234 0.00278753263633103 0.00557506527266206 -1.84301342041422 +"11303" -0.0558958943607024 17.886791401216 -1.30108531275582 0.205582481502277 0.254491025872966 -6.49241240578 +"11305" -0.0606991650996669 18.1585474109909 -1.28203791127301 0.212075854894138 0.254491025872966 -6.42090197700496 +"11302" -0.035023968220445 9.78883119065989 -0.236945963165271 0.814709535394086 0.814709535394086 -6.09497670655939 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_Mut-WT_2fact.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/limma-voom_Mut-WT_2fact.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"GeneID" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" +"11287" 0.190521683937302 17.6546448244617 14.4538942795641 5.93483727833391e-09 3.56090236700035e-08 96.5864491179047 +"11298" -0.13987741320075 17.6747285193431 -7.7190169464239 5.41139783114199e-06 1.6234193493426e-05 22.3495333961476 +"11304" 0.459011254726059 15.5254133001226 5.6408319840902 0.00010884906092378 0.000217698121847559 8.76657226635715 +"11303" -0.0641599901594248 17.886791401216 -2.9900818153928 0.0112725655419901 0.0169088483129851 -2.70089035288878 +"11305" -0.0651479753016169 18.1585474109909 -2.28935282063866 0.0409794711446066 0.0491753653735279 -4.2713352660451 +"11302" -0.0358817134644287 9.78883119065989 -0.439436789626843 0.668154169055813 0.668154169055813 -5.75838315483931 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_Mut-WT_2fact_anno.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/limma-voom_Mut-WT_2fact_anno.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"EntrezID" "Symbol" "GeneName" "Chr" "Length" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" +11287 "Pzp" "pregnancy zone protein" 6 4681 0.190521683937302 17.6546448244617 15.1152647604854 3.5605743515492e-09 2.13634461092952e-08 106.319792304784 +11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 -0.139877413200757 17.6747285193431 -8.49164953574146 2.03124167559177e-06 6.0937250267753e-06 28.5167891813121 +11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 0.459011254726057 15.5254133001226 5.60316118539212 0.000115556485215252 0.000231112970430504 8.56249981126828 +11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 -0.0641599901594141 17.886791401216 -2.92798536696768 0.0126512435710263 0.0189768653565394 -2.86386681629442 +11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 -0.0651479753016169 18.1585474109909 -2.03911882030581 0.0640903140266962 0.0769083768320354 -4.69855556350315 +11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 -0.0358817134644287 9.78883119065989 -0.43940476739557 0.668176726641997 0.668176726641997 -5.75841999159995 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_Mut-WT_anno.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/limma-voom_Mut-WT_anno.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"EntrezID" "Symbol" "GeneName" "Chr" "Length" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" +11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 0.457332061341022 15.5254133001226 6.50459574633635 9.98720685007144e-07 5.99232411004286e-06 14.0741948485867 +11287 "Pzp" "pregnancy zone protein" 6 4681 0.190749727701785 17.6546448244617 5.09535410066427 3.26518807653921e-05 9.79556422961764e-05 5.46773893802514 +11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 -0.138014418336201 17.6747285193431 -3.3316848584234 0.00278753263633103 0.00557506527266206 -1.84301342041422 +11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 -0.0558958943607024 17.886791401216 -1.30108531275582 0.205582481502277 0.254491025872966 -6.49241240578 +11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 -0.0606991650996669 18.1585474109909 -1.28203791127301 0.212075854894138 0.254491025872966 -6.42090197700496 +11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 -0.035023968220445 9.78883119065989 -0.236945963165271 0.814709535394086 0.814709535394086 -6.09497670655939 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_Mut-WTanno.tsv --- a/test-data/limma-voom_Mut-WTanno.tsv Thu Sep 07 05:27:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -"EntrezID" "Symbol" "GeneName" "Chr" "Length" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" -11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 0.457332061341026 15.5254133001226 6.50459574633681 9.98720685006039e-07 5.99232411003624e-06 14.0741948485896 -11287 "Pzp" "pregnancy zone protein" 6 4681 0.190749727701785 17.6546448244617 5.09535410066402 3.26518807654125e-05 9.79556422962375e-05 5.46773893802392 -11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 -0.138014418336201 17.6747285193431 -3.33168485842331 0.00278753263633162 0.00557506527266324 -1.84301342041449 -11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 -0.0558958943606989 17.886791401216 -1.30108531275576 0.205582481502297 0.254491025872973 -6.4924124057801 -11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 -0.0606991650996633 18.1585474109909 -1.28203791127299 0.212075854894144 0.254491025872973 -6.42090197700503 -11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 -0.0350239682204432 9.78883119065989 -0.236945963165269 0.814709535394087 0.814709535394087 -6.09497670655944 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_Mut-WTmultifact.tsv --- a/test-data/limma-voom_Mut-WTmultifact.tsv Thu Sep 07 05:27:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -"GeneID" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" -"11287" 0.190521683937291 17.6546448244617 14.4538942795625 5.93483727834149e-09 3.56090236700489e-08 96.5864491178815 -"11298" -0.139877413200757 17.6747285193431 -7.71901694642401 5.4113978311412e-06 1.62341934934236e-05 22.3495333961486 -"11304" 0.459011254726061 15.5254133001226 5.64083198409048 0.000108849060923731 0.000217698121847462 8.76657226635859 -"11303" -0.0641599901594212 17.886791401216 -2.99008181539252 0.0112725655419959 0.0169088483129939 -2.70089035288952 -"11305" -0.0651479753016204 18.1585474109909 -2.28935282063873 0.0409794711446019 0.0491753653735222 -4.27133526604488 -"11302" -0.035881713464434 9.78883119065989 -0.439436789626921 0.668154169055758 0.668154169055758 -5.75838315483926 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_WT-Mut.tsv --- a/test-data/limma-voom_WT-Mut.tsv Thu Sep 07 05:27:27 2017 -0400 +++ b/test-data/limma-voom_WT-Mut.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ "GeneID" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" -"11304" -0.457332061341026 15.5254133001226 -6.50459574633681 9.98720685006039e-07 5.99232411003624e-06 14.0741948485896 -"11287" -0.190749727701785 17.6546448244617 -5.09535410066402 3.26518807654125e-05 9.79556422962375e-05 5.46773893802392 -"11298" 0.138014418336201 17.6747285193431 3.33168485842331 0.00278753263633162 0.00557506527266324 -1.84301342041449 -"11303" 0.0558958943606989 17.886791401216 1.30108531275576 0.205582481502297 0.254491025872973 -6.4924124057801 -"11305" 0.0606991650996633 18.1585474109909 1.28203791127299 0.212075854894144 0.254491025872973 -6.42090197700503 -"11302" 0.0350239682204432 9.78883119065989 0.236945963165269 0.814709535394087 0.814709535394087 -6.09497670655944 +"11304" -0.457332061341022 15.5254133001226 -6.50459574633635 9.98720685007144e-07 5.99232411004286e-06 14.0741948485867 +"11287" -0.190749727701785 17.6546448244617 -5.09535410066427 3.26518807653921e-05 9.79556422961764e-05 5.46773893802514 +"11298" 0.138014418336201 17.6747285193431 3.3316848584234 0.00278753263633103 0.00557506527266206 -1.84301342041422 +"11303" 0.0558958943607024 17.886791401216 1.30108531275582 0.205582481502277 0.254491025872966 -6.49241240578 +"11305" 0.0606991650996669 18.1585474109909 1.28203791127301 0.212075854894138 0.254491025872966 -6.42090197700496 +"11302" 0.035023968220445 9.78883119065989 0.236945963165271 0.814709535394086 0.814709535394086 -6.09497670655939 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_WT-Mut_2fact_anno.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/limma-voom_WT-Mut_2fact_anno.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"EntrezID" "Symbol" "GeneName" "Chr" "Length" "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" +11287 "Pzp" "pregnancy zone protein" 6 4681 -0.190521683937302 17.6546448244617 -15.1152647604854 3.5605743515492e-09 2.13634461092952e-08 106.319792304784 +11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 0.139877413200757 17.6747285193431 8.49164953574146 2.03124167559177e-06 6.0937250267753e-06 28.5167891813121 +11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 -0.459011254726057 15.5254133001226 -5.60316118539212 0.000115556485215252 0.000231112970430504 8.56249981126828 +11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 0.0641599901594141 17.886791401216 2.92798536696768 0.0126512435710263 0.0189768653565394 -2.86386681629442 +11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 0.0651479753016169 18.1585474109909 2.03911882030581 0.0640903140266962 0.0769083768320354 -4.69855556350315 +11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 0.0358817134644287 9.78883119065989 0.43940476739557 0.668176726641997 0.668176726641997 -5.75841999159995 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_normcounts.tsv --- a/test-data/limma-voom_normcounts.tsv Thu Sep 07 05:27:27 2017 -0400 +++ b/test-data/limma-voom_normcounts.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ -"GeneID" "WT1" "WT2" "WT3" "Mut1" "Mut2" "Mut3" -"11287" 17.6076545522668 17.5079905058358 17.5639197719462 17.7719335903598 17.7105244453357 17.7658460810258 -"11298" 17.7727137985373 17.6986875511432 17.7598828784201 17.6506532355915 17.5520012519588 17.6144324004081 -"11302" 9.57719962386619 10.0175525101992 9.82560228478005 9.71615817858834 9.91760904198188 9.67886550454371 -"11303" 17.9125899785601 17.8773613214092 17.955228759658 17.8774046020864 17.7865502833631 17.911613462219 -"11304" 15.354518172169 15.2178020484983 15.3174553811097 15.7545783969022 15.8519803740125 15.6561454280436 -"11305" 18.1808259688524 18.1818679259847 18.2026681768366 18.0401341021246 18.1408682071359 18.204920085011 +"GeneID" "Mut1" "Mut2" "Mut3" "WT1" "WT2" "WT3" +"11287" 17.7719335903598 17.7105244453357 17.7658460810258 17.6076545522668 17.5079905058358 17.5639197719462 +"11298" 17.6506532355915 17.5520012519588 17.6144324004081 17.7727137985373 17.6986875511432 17.7598828784201 +"11302" 9.71615817858834 9.91760904198188 9.67886550454371 9.57719962386619 10.0175525101992 9.82560228478005 +"11303" 17.8774046020864 17.7865502833631 17.911613462219 17.9125899785601 17.8773613214092 17.955228759658 +"11304" 15.7545783969022 15.8519803740125 15.6561454280436 15.354518172169 15.2178020484983 15.3174553811097 +"11305" 18.0401341021246 18.1408682071359 18.204920085011 18.1808259688524 18.1818679259847 18.2026681768366 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/limma-voom_normcounts_anno.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/limma-voom_normcounts_anno.tsv Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"EntrezID" "Symbol" "GeneName" "Chr" "Length" "Mut1" "Mut2" "Mut3" "WT1" "WT2" "WT3" +11287 "Pzp" "pregnancy zone protein" 6 4681 17.7719335903598 17.7105244453357 17.7658460810258 17.6076545522668 17.5079905058358 17.5639197719462 +11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 17.6506532355915 17.5520012519588 17.6144324004081 17.7727137985373 17.6986875511432 17.7598828784201 +11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 9.71615817858834 9.91760904198188 9.67886550454371 9.57719962386619 10.0175525101992 9.82560228478005 +11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 17.8774046020864 17.7865502833631 17.911613462219 17.9125899785601 17.8773613214092 17.955228759658 +11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 15.7545783969022 15.8519803740125 15.6561454280436 15.354518172169 15.2178020484983 15.3174553811097 +11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 18.0401341021246 18.1408682071359 18.204920085011 18.1808259688524 18.1818679259847 18.2026681768366 |
| b |
| diff -r a330ddf43861 -r 38aab66ae5cb test-data/matrix.txt --- a/test-data/matrix.txt Thu Sep 07 05:27:27 2017 -0400 +++ b/test-data/matrix.txt Wed Jan 31 12:45:42 2018 -0500 |
| b |
| @@ -1,7 +1,7 @@ -GeneID WT1 WT2 WT3 Mut1 Mut2 Mut3 -11287 1699 1528 1601 1463 1441 1495 -11298 1905 1744 1834 1345 1291 1346 -11302 6 8 7 5 6 5 -11303 2099 1974 2100 1574 1519 1654 -11304 356 312 337 361 397 346 -11305 2528 2438 2493 1762 1942 2027 +GeneID Mut1 Mut2 Mut3 WT1 WT2 WT3 +11287 1463 1441 1495 1699 1528 1601 +11298 1345 1291 1346 1905 1744 1834 +11302 5 6 5 6 8 7 +11303 1574 1519 1654 2099 1974 2100 +11304 361 397 346 356 312 337 +11305 1762 1942 2027 2528 2438 2493 |