Mercurial > repos > lgueguen > sartools

comparison template_script_edgeR_CL.r @ 3:de6d0b7c17af draft

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release 1.6.3
author lgueguen
date Mon, 01 Oct 2018 05:07:56 -0400
parents 581d217c7337
children
comparison
equal deleted inserted replaced
2:d86ccac2a660 3:de6d0b7c17af
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)