Mercurial > repos > lgueguen > sartools

comparison template_script_DESeq2_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 05c9b1a7f44e
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_DESeq2_CL.r -r raw -v group -c T0 > log.txt 2>&1
5 # Rscript template_script_DESeq2_CL.r -r raw -v group -c T0
6
7 # to get help:
8 # Rscript template_script_DESeq2_CL.r --help
9
10 ################################################################################ 1 ################################################################################
11 ### R script to compare several conditions with the SARTools and DESeq2 packages 2 ### R script to compare several conditions with the SARTools and DESeq2 packages
12 ### Hugo Varet 3 ### Hugo Varet
13 ### April 20th, 2015 4 ### March 20th, 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_DESeq2_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
60 help="blocking factor [default: %default] or \"batch\" for example"), 52 help="blocking factor [default: %default] or \"batch\" for example"),
61 53
62 make_option(c("-f", "--fitType"), 54 make_option(c("-f", "--fitType"),
63 default="parametric", 55 default="parametric",
64 dest="fitType", 56 dest="fitType",
65 help="mean-variance relationship: [default: %default] or local"), 57 help="mean-variance relationship: [default: %default], local or mean"),
66 58
67 make_option(c("-o", "--cooksCutoff"), 59 make_option(c("-o", "--cooksCutoff"),
68 default=TRUE, 60 default=TRUE,
69 dest="cooksCutoff", 61 dest="cooksCutoff",
70 help="perform the outliers detection (default is TRUE)"), 62 help="perform the outliers detection (default is TRUE)"),
95 help="median or shorth to estimate the size factors [default: %default]"), 87 help="median or shorth to estimate the size factors [default: %default]"),
96 88
97 make_option(c("-C", "--colors"), 89 make_option(c("-C", "--colors"),
98 default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange", 90 default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
99 dest="cols", 91 dest="cols",
100 help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]") 92 help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"),
93
94 make_option(c("-g", "--forceCairoGraph"),
95 action="store_true",
96 default=FALSE,
97 dest="forceCairoGraph",
98 help="activate cairo type")
99
101 ) 100 )
102 101
103 # now parse the command line to check which option is given and get associated values 102 # now parse the command line to check which option is given and get associated values
104 parser <- OptionParser(usage="usage: %prog [options]", 103 parser <- OptionParser(usage="usage: %prog [options]",
105 option_list=option_list, 104 option_list=option_list,
115 rawDir <- opt$rawDir # path to the directory containing raw counts files 114 rawDir <- opt$rawDir # path to the directory containing raw counts files
116 featuresToRemove <- unlist(strsplit(opt$FTR, ",")) # names of the features to be removed (specific HTSeq-count information and rRNA for example) 115 featuresToRemove <- unlist(strsplit(opt$FTR, ",")) # names of the features to be removed (specific HTSeq-count information and rRNA for example)
117 varInt <- opt$varInt # factor of interest 116 varInt <- opt$varInt # factor of interest
118 condRef <- opt$condRef # reference biological condition 117 condRef <- opt$condRef # reference biological condition
119 batch <- opt$batch # blocking factor: NULL (default) or "batch" for example 118 batch <- opt$batch # blocking factor: NULL (default) or "batch" for example
120 fitType <- opt$fitType # mean-variance relationship: "parametric" (default) or "local" 119 fitType <- opt$fitType # mean-variance relationship: "parametric" (default), "local" or "mean"
121 cooksCutoff <- opt$cooksCutoff # outliers detection threshold (NULL to let DESeq2 choosing it) 120 cooksCutoff <- opt$cooksCutoff # outliers detection threshold (NULL to let DESeq2 choosing it)
122 independentFiltering <- opt$independentFiltering # TRUE/FALSE to perform independent filtering (default is TRUE) 121 independentFiltering <- opt$independentFiltering # TRUE/FALSE to perform independent filtering (default is TRUE)
123 alpha <- as.numeric(opt$alpha) # threshold of statistical significance 122 alpha <- as.numeric(opt$alpha) # threshold of statistical significance
124 pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY" 123 pAdjustMethod <- opt$pAdjustMethod # p-value adjustment method: "BH" (default) or "BY"
125 typeTrans <- opt$typeTrans # transformation for PCA/clustering: "VST" ou "rlog" 124 typeTrans <- opt$typeTrans # transformation for PCA/clustering: "VST" ou "rlog"
126 locfunc <- opt$locfunc # "median" (default) or "shorth" to estimate the size factors 125 locfunc <- opt$locfunc # "median" (default) or "shorth" to estimate the size factors
127 colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots 126 colors <- unlist(strsplit(opt$cols, ",")) # vector of colors of each biologicial condition on the plots
128 127 forceCairoGraph <- opt$forceCairoGraph # force cairo as plotting device if enabled
129 # print(paste("workDir", workDir)) 128 # print(paste("workDir", workDir))
130 # print(paste("projectName", projectName)) 129 # print(paste("projectName", projectName))
131 # print(paste("author", author)) 130 # print(paste("author", author))
132 # print(paste("targetFile", targetFile)) 131 # print(paste("targetFile", targetFile))
133 # print(paste("rawDir", rawDir)) 132 # print(paste("rawDir", rawDir))
147 ################################################################################ 146 ################################################################################
148 ### running script ### 147 ### running script ###
149 ################################################################################ 148 ################################################################################
150 # setwd(workDir) 149 # setwd(workDir)
151 library(SARTools) 150 library(SARTools)
151 if (forceCairoGraph) options(bitmapType="cairo")
152 152
153 # checking parameters 153 # checking parameters
154 problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile, 154 problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,
155 rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt, 155 rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
156 condRef=condRef,batch=batch,fitType=fitType,cooksCutoff=cooksCutoff, 156 condRef=condRef,batch=batch,fitType=fitType,cooksCutoff=cooksCutoff,