readBedgraph.R

library(BiSeq)

readBedgraph <- function(inputDirectory, nSamples = 8) {

	## get list of file names
	fileNames <- list.files(path = inputDirectory, pattern = ".bedGraph")
	## parse sample name from file name
    	sampleNames <- sapply(fileNames,function(fileName) {
				gsub("_r123_R1_val_1.fq_bismark_bt2_pe.bedGraph", "", fileName)
				}, USE.NAMES = FALSE)
	## label samples
	colData <- data.frame(group = rep(c("control", "cancer"), nSamples), row.names = sampleNames)
	rawBSObj <- readBismark(fileNames, colData)
	
	return(rawBSObj)
}