docker and new script

codescript/EPIC.raw.R

+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("stats"))
+
+# specify our desired options in a list
+# by default OptionParser will add an help option equivalent to 
+# make_option(c("-h", "--help"), action="store_true", default=FALSE, 
+#               help="Show this help message and exit")
+
+option_list <- list( 
+  make_option(c("-p", "--prefix"), type="character",default="./",
+              help="The output files prefix [default ./]"),
+  make_option(c("-i", "--input"),type="character", default=NULL,
+              help="The directory of input EPIC files. required!")
+)
+
+# get command line options, if help option encountered print help and exit,
+# otherwise if options not found on command line then set defaults, 
+opt <- parse_args(OptionParser(option_list=option_list))
+
+# load libraries
+
+library("minfi")
+library("IlluminaHumanMethylationEPICmanifest")
+library("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
+
+## 1. data import
+targets <- read.metharray.sheet(opt$input)
+rgSet <- read.metharray.exp(targets = targets)
+targets$ID <- paste(targets$Sample_Group,targets$Sample_Name,sep=".")
+sampleNames(rgSet) <- targets$ID
+#phenoData <- pData(rgSet)
+message("data import:finished")
+
+## 2. Quality control
+# 2.1 qc report by minfi
+# qcReport(rgSet, sampNames=targets$ID, sampGroups=targets$Sample_Group,pdf="qcReport.pdf")
+          
+# 2.2 data filtering
+# get detected p value
+# a. remove samples with average p value less than 0.05
+detP <- detectionP(rgSet)
+message("calculate p value:finished")
+
+# raw
+mSetRaw <- preprocessRaw(rgSet)
+raw_mVals <- getM(mSetRaw)
+raw_bVals <- getBeta(mSetRaw)
+message("m value and beta value output:finished")
+
+# write output
+message("saving R data")
+rdata_filename = paste(opt$prefix, '.RData',sep="")
+save(rgSet, targets, detP, file = rdata_filename)
+message("writing raw table")
+m_raw_filename = paste(opt$prefix,'.raw.mVal.txt',sep="")
+write.table(raw_mVals,m_raw_filename,col.names = T,row.names = T,sep="\t",quote=F)
+b_raw_filename = paste(opt$prefix,'.raw.bVal.txt',sep="")
+write.table(raw_bVals,b_raw_filename,col.names = T,row.names = T,sep="\t",quote=F)