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view deseq/differential_expression_analysis_pipeline_for_rnaseq_data-a03838a6eb54/DiffExpAnal/DESeqTools/loadCountData.R @ 10:6e573fd3c41b draft
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author | yufei-luo |
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date | Mon, 13 May 2013 10:06:30 -0400 |
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# loadCountData # loads counts, one file per lane # file names from target file # input : target # output : raw count table # created Feb 6th, 2012 # modified May 2nd, 2012 (colnames -> target$label) # Marie-Agnes Dillies loadCountData <- function(target, header){ require(DESeq) fileNames <- target$files if(header!=0){ #rawCounts <- read.table(as.character(paste(rawDir,target$files[1],sep="/")), sep="\t", header=TRUE) rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t", header=TRUE) } else if(header==0){ rawCounts <- read.table(as.character(target$files[1],sep="/"), sep="\t")} colnames(rawCounts) <- c("Id", as.character(target$label[1])) for (i in 2:length(fileNames)){ if(header!=0){ tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t", header=TRUE) } else if(header==0){ tmp <- read.table(as.character(target$files[i],sep="/"), sep="\t")} colnames(tmp) <- c("Id", as.character(target$label[i])) rawCounts <- merge(rawCounts, tmp, by="Id", all=T) } rawCounts[is.na(rawCounts)] <- 0 return(rawCounts) }