Mercurial > repos > iuc > dexseq
annotate dexseq.R @ 6:9fd8b69e6e68 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 68251c72950b8f31e906cf2c2983952ed3eaec1a
author | iuc |
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date | Tue, 26 Feb 2019 10:50:15 -0500 |
parents | 278b189248cd |
children | 62adf13b86ea |
rev | line source |
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4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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1 ## Setup R error handling to go to stderr |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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5 |
2
6e8b61c54ff3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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6 suppressPackageStartupMessages({ |
6e8b61c54ff3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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7 library("DEXSeq") |
6e8b61c54ff3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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8 library('getopt') |
6e8b61c54ff3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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9 library('rjson') |
6e8b61c54ff3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
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10 }) |
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4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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11 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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12 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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13 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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14 args <- commandArgs(trailingOnly = TRUE) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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15 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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16 #get options, using the spec as defined by the enclosed list. |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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17 #we read the options from the default: commandArgs(TRUE). |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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18 spec = matrix(c( |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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19 'verbose', 'v', 2, "integer", |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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20 'help', 'h', 0, "logical", |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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21 'gtf', 'a', 1, "character", |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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22 'outfile', 'o', 1, "character", |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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23 'reportdir', 'r', 1, "character", |
5
278b189248cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
iuc
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24 'rds', 'd', 1, "character", |
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4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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25 'factors', 'f', 1, "character", |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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26 'threads', 'p', 1, "integer", |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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27 'fdr', 'c', 1, "double" |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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28 ), byrow=TRUE, ncol=4); |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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29 opt = getopt(spec); |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
parents:
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30 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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31 # if help was asked for print a friendly message |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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32 # and exit with a non-zero error code |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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33 if ( !is.null(opt$help) ) { |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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34 cat(getopt(spec, usage=TRUE)); |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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35 q(status=1); |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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36 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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37 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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38 trim <- function (x) gsub("^\\s+|\\s+$", "", x) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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39 opt$samples <- trim(opt$samples) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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40 opt$factors <- trim(opt$factors) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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41 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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42 parser <- newJSONParser() |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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43 parser$addData( opt$factors ) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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44 factorsList <- parser$getObject() |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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45 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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46 sampleTable<-data.frame() |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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47 countFiles<-c() |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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48 factorNames<-c() |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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49 primaryFactor<-"" |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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50 for(factor in factorsList){ |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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51 factorName<-factor[[1]] |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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52 factorNames<-append(factorNames, paste(factorName,"exon",sep=":")) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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53 factorValuesMapList<-factor[[2]] |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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54 c = length(factorValuesMapList) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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55 for (factorValuesMap in factorValuesMapList){ |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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56 for(files in factorValuesMap){ |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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57 for(file in files){ |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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58 if(primaryFactor == "") { |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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59 countFiles<-append(countFiles,file) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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60 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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61 sampleTable[basename(file),factorName]<-paste(c,names(factorValuesMap),sep="_") |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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62 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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63 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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64 c = c-1 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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65 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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66 if(primaryFactor == ""){ |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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67 primaryFactor <- factorName |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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68 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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69 } |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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70 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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71 factorNames<-append(factorNames,"exon") |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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72 factorNames<-append(factorNames,"sample") |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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73 factorNames<-rev(factorNames) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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74 formulaFullModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ ")) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
iuc
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75 factorNames <- head(factorNames,-1) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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76 formulaReducedModel <- as.formula(paste("", paste(factorNames, collapse=" + "), sep=" ~ ")) |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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77 |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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78 sampleTable |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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79 formulaFullModel |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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80 formulaReducedModel |
4ca0e679f21e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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81 primaryFactor |
4ca0e679f21e
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82 countFiles |
4ca0e679f21e
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83 opt$reportdir |
4ca0e679f21e
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84 opt$threads |
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85 getwd() |
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86 |
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87 dxd = DEXSeqDataSetFromHTSeq(countFiles, sampleData=sampleTable, design= formulaFullModel, flattenedfile=opt$gtf) |
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88 |
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89 colData(dxd) |
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90 dxd <- estimateSizeFactors(dxd) |
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91 print("Estimated size factors") |
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92 sizeFactors(dxd) |
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93 BPPARAM=MulticoreParam(workers=opt$threads) |
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94 dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM) |
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95 print("Estimated dispersions") |
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96 dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM) |
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97 print("tested for DEU") |
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98 dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM) |
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99 print("Estimated fold changes") |
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100 res <- DEXSeqResults(dxd) |
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101 print("Results") |
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102 table(res$padj <= opt$fdr) |
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103 resSorted <- res[order(res$padj),] |
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104 head(resSorted) |
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105 |
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106 export_table <- as.data.frame(resSorted) |
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107 last_column <- ncol(export_table) |
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108 for(i in 1:nrow(export_table)) { |
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109 export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ") |
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110 } |
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111 write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE) |
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112 print("Written Results") |
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113 |
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114 if ( !is.null(opt$rds) ) { |
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115 saveRDS(res, file="DEXSeqResults.rds") |
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116 } |
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117 |
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118 if ( !is.null(opt$reportdir) ) { |
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119 DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) |
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120 } |
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121 sessionInfo() |