--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/template_script_edgeR_CL.r	Fri Jul 22 05:39:13 2016 -0400
@@ -0,0 +1,175 @@
+#!/local/gensoft2/exe/R/3.1.2/bin/Rscript
+
+# to run this script, use one of these commands:
+# Rscript --no-save --no-restore --verbose template_script_edgeR_CL.r -r raw -v group -c T0 > log.txt 2>&1
+# Rscript template_script_edgeR_CL.r -r raw -v group -c T0
+
+# to get help:
+# Rscript template_script_edgeR_CL.r --help
+
+################################################################################
+### R script to compare several conditions with the SARTools and edgeR packages
+### Hugo Varet
+### April 20th, 2015
+### designed to be executed with SARTools 1.1.0
+################################################################################
+
+rm(list=ls())                                        # remove all the objects from the R session
+library(optparse)                                    # to run the script in command lines
+
+# options list with associated default value.
+option_list <- list( 
+make_option(c("-P", "--projectName"),
+			default=basename(getwd()),
+			dest="projectName",
+			help="name of the project used for the report [default: name of the current directory]."),
+
+make_option(c("-A", "--author"),
+			default=Sys.info()[7],
+			dest="author",
+			help="name of the report author [default: %default]."),
+
+make_option(c("-t", "--targetFile"),
+			default="target.txt",
+			dest="targetFile",
+			help="path to the design/target file [default: %default]."),
+
+make_option(c("-r", "--rawDir"),
+			default="raw",
+			dest="rawDir",
+			help="path to the directory containing the HTSeq files [default: %default]."),		
+
+make_option(c("-F", "--featuresToRemove"),
+			default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
+			dest="FTR",
+			help="names of the features to be removed, more than once can be specified [default: %default]"),
+			
+make_option(c("-v", "--varInt"),
+			default="group",
+			dest="varInt", 
+			help="factor of interest [default: %default]"),
+
+make_option(c("-c", "--condRef"),
+			default="WT",
+			dest="condRef",
+			help="reference biological condition [default: %default]"),
+
+make_option(c("-b", "--batch"),
+			default=NULL,
+			dest="batch",
+			help="blocking factor [default: %default] or \"batch\" for example"),
+
+make_option(c("-a", "--alpha"),
+			default=0.05,
+			dest="alpha", 
+			help="threshold of statistical significance [default: %default]"),
+
+make_option(c("-p", "--pAdjustMethod"),
+			default="BH",
+			dest="pAdjustMethod", 
+			help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
+
+make_option(c("-m", "--cpmCutoff"),
+			default=1,
+			dest="cpmCutoff", 
+			help="counts-per-million cut-off to filter low counts"),
+			
+make_option(c("-g", "--gene.selection"),
+			default="pairwise",
+			dest="gene.selection", 
+			help="selection of the features in MDSPlot [default: %default]"),
+			
+make_option(c("-n", "--normalizationMethod"),
+			default="TMM",
+			dest="normalizationMethod", 
+			help="normalization method in calcNormFactors: \"TMM\", \"RLE\" or \"upperquartile\" [default: %default]"),
+
+make_option(c("-C", "--colors"),
+			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
+			dest="cols",
+			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
+)
+
+# now parse the command line to check which option is given and get associated values
+parser <- OptionParser(usage="usage: %prog [options]",
+					   option_list=option_list, 
+					   description="Compare two or more biological conditions in a RNA-Seq framework with edgeR.",
+					   epilogue="For comments, bug reports etc... please contact Hugo Varet <hugo.varet@pasteur.fr>")
+opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
+
+# get options and arguments
+workDir <- getwd()
+projectName <- opt$projectName                       # name of the project
+author <- opt$author	                             # author of the statistical analysis/report
+targetFile <- opt$targetFile                         # path to the design/target file
+rawDir <- opt$rawDir								 # path to the directory containing raw counts files
+featuresToRemove <- unlist(strsplit(opt$FTR, ","))   # names of the features to be removed (specific HTSeq-count information and rRNA for example)
+varInt <- opt$varInt                                 # factor of interest
+condRef <- opt$condRef                               # reference biological condition
+batch <- opt$batch                                   # blocking factor: NULL (default) or "batch" for example
+alpha <- as.numeric(opt$alpha)                       # threshold of statistical significance
+pAdjustMethod <- opt$pAdjustMethod                   # p-value adjustment method: "BH" (default) or "BY"
+gene.selection <- opt$gene.selection                 # selection of the features in MDSPlot
+normalizationMethod <- opt$normalizationMethod       # normalization method in calcNormFactors
+cpmCutoff <- opt$cpmCutoff                           # counts-per-million cut-off to filter low counts
+colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
+
+# print(paste("workDir", workDir))
+# print(paste("projectName", projectName))
+# print(paste("author", author))
+# print(paste("targetFile", targetFile))
+# print(paste("rawDir", rawDir))
+# print(paste("varInt", varInt))
+# print(paste("condRef", condRef))
+# print(paste("batch", batch))
+# print(paste("alpha", alpha))
+# print(paste("pAdjustMethod", pAdjustMethod))
+# print(paste("featuresToRemove", featuresToRemove))
+# print(paste("colors", colors))
+# print(paste("gene.selection", gene.selection))
+# print(paste("normalizationMethod", normalizationMethod))
+# print(paste("cpmCutoff", cpmCutoff))
+
+################################################################################
+###                             running script                               ###
+################################################################################
+# setwd(workDir)
+library(SARTools)
+
+# checking parameters
+problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,
+                      rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
+                      condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod,
+                      cpmCutoff=cpmCutoff,gene.selection=gene.selection,
+                      normalizationMethod=normalizationMethod,colors=colors)
+if (problem) quit(save="yes")
+					  
+# loading target file
+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
+
+# loading counts
+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
+
+# description plots
+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
+
+# edgeR analysis
+out.edgeR <- run.edgeR(counts=counts, target=target, varInt=varInt, condRef=condRef,
+                       batch=batch, cpmCutoff=cpmCutoff, normalizationMethod=normalizationMethod,
+                       pAdjustMethod=pAdjustMethod)
+
+# MDS + clustering
+exploreCounts(object=out.edgeR$dge, group=target[,varInt], gene.selection=gene.selection, col=colors)
+
+# summary of the analysis (boxplots, dispersions, export table, nDiffTotal, histograms, MA plot)
+summaryResults <- summarizeResults.edgeR(out.edgeR, group=target[,varInt], counts=counts, alpha=alpha, col=colors)
+
+# save image of the R session
+save.image(file=paste0(projectName, ".RData"))
+
+# generating HTML report
+writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults,
+                  majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
+                  targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
+                  condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, colors=colors,
+                  gene.selection=gene.selection, normalizationMethod=normalizationMethod)