Mercurial > repos > lgueguen > sartools
comparison template_script_edgeR_CL.r @ 3:de6d0b7c17af draft
release 1.6.3
| author | lgueguen |
|---|---|
| date | Mon, 01 Oct 2018 05:07:56 -0400 |
| parents | 581d217c7337 |
| children |
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| 2:d86ccac2a660 | 3:de6d0b7c17af |
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| 1 #!/local/gensoft2/exe/R/3.1.2/bin/Rscript | |
| 2 | |
| 3 # to run this script, use one of these commands: | |
| 4 # Rscript --no-save --no-restore --verbose template_script_edgeR_CL.r -r raw -v group -c T0 > log.txt 2>&1 | |
| 5 # Rscript template_script_edgeR_CL.r -r raw -v group -c T0 | |
| 6 | |
| 7 # to get help: | |
| 8 # Rscript template_script_edgeR_CL.r --help | |
| 9 | |
| 10 ################################################################################ | 1 ################################################################################ |
| 11 ### R script to compare several conditions with the SARTools and edgeR packages | 2 ### R script to compare several conditions with the SARTools and edgeR packages |
| 12 ### Hugo Varet | 3 ### Hugo Varet |
| 13 ### April 20th, 2015 | 4 ### May 16th, 2018 |
| 14 ### designed to be executed with SARTools 1.1.0 | 5 ### designed to be executed with SARTools 1.6.3 |
| 6 ### run "Rscript template_script_edgeR_CL.r --help" to get some help | |
| 15 ################################################################################ | 7 ################################################################################ |
| 16 | 8 |
| 17 rm(list=ls()) # remove all the objects from the R session | 9 rm(list=ls()) # remove all the objects from the R session |
| 18 library(optparse) # to run the script in command lines | 10 library(optparse) # to run the script in command lines |
| 19 | 11 |
| 85 help="normalization method in calcNormFactors: \"TMM\", \"RLE\" or \"upperquartile\" [default: %default]"), | 77 help="normalization method in calcNormFactors: \"TMM\", \"RLE\" or \"upperquartile\" [default: %default]"), |
| 86 | 78 |
| 87 make_option(c("-C", "--colors"), | 79 make_option(c("-C", "--colors"), |
| 88 default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange", | 80 default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange", |
| 89 dest="cols", | 81 dest="cols", |
| 90 help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]") | 82 help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"), |
| 83 | |
| 84 make_option(c("-f", "--forceCairoGraph"), | |
| 85 action="store_true", | |
| 86 default=FALSE, | |
| 87 dest="forceCairoGraph", | |
| 88 help="activate cairo type") | |
| 91 ) | 89 ) |
| 92 | 90 |
| 93 # now parse the command line to check which option is given and get associated values | 91 # now parse the command line to check which option is given and get associated values |
| 94 parser <- OptionParser(usage="usage: %prog [options]", | 92 parser <- OptionParser(usage="usage: %prog [options]", |
| 95 option_list=option_list, | 93 option_list=option_list, |
| 111 pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY" | 109 pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY" |
| 112 gene.selection <- opt$gene.selection # selection of the features in MDSPlot | 110 gene.selection <- opt$gene.selection # selection of the features in MDSPlot |
| 113 normalizationMethod <- opt$normalizationMethod # normalization method in calcNormFactors | 111 normalizationMethod <- opt$normalizationMethod # normalization method in calcNormFactors |
| 114 cpmCutoff <- opt$cpmCutoff # counts-per-million cut-off to filter low counts | 112 cpmCutoff <- opt$cpmCutoff # counts-per-million cut-off to filter low counts |
| 115 colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots | 113 colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots |
| 116 | 114 forceCairoGraph <- opt$forceCairoGraph # force cairo as plotting device if enabled |
| 117 # print(paste("workDir", workDir)) | 115 # print(paste("workDir", workDir)) |
| 118 # print(paste("projectName", projectName)) | 116 # print(paste("projectName", projectName)) |
| 119 # print(paste("author", author)) | 117 # print(paste("author", author)) |
| 120 # print(paste("targetFile", targetFile)) | 118 # print(paste("targetFile", targetFile)) |
| 121 # print(paste("rawDir", rawDir)) | 119 # print(paste("rawDir", rawDir)) |
| 133 ################################################################################ | 131 ################################################################################ |
| 134 ### running script ### | 132 ### running script ### |
| 135 ################################################################################ | 133 ################################################################################ |
| 136 # setwd(workDir) | 134 # setwd(workDir) |
| 137 library(SARTools) | 135 library(SARTools) |
| 136 if (forceCairoGraph) options(bitmapType="cairo") | |
| 138 | 137 |
| 139 # checking parameters | 138 # checking parameters |
| 140 problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile, | 139 problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile, |
| 141 rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt, | 140 rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt, |
| 142 condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod, | 141 condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod, |
| 169 | 168 |
| 170 # generating HTML report | 169 # generating HTML report |
| 171 writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults, | 170 writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults, |
| 172 majSequences=majSequences, workDir=workDir, projectName=projectName, author=author, | 171 majSequences=majSequences, workDir=workDir, projectName=projectName, author=author, |
| 173 targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt, | 172 targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt, |
| 174 condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, colors=colors, | 173 condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, cpmCutoff=cpmCutoff, |
| 175 gene.selection=gene.selection, normalizationMethod=normalizationMethod) | 174 colors=colors, gene.selection=gene.selection, normalizationMethod=normalizationMethod) |