RAPIDR (version 0.1.1)

writeCleanedCountsFile: writeCleanedCountsFiles

Description

This function takes a binned.counts.file and applies GC correction or PCA correction and writes out the resulting binned counts as a a new file

Usage

writeCleanedCountsFile(binned.counts.file, cleaned.binned.counts.fname, gcContentFile, gcCorrect = FALSE, PCA = FALSE)

Arguments

binned.counts.file

file name of the binned counts. The binned counts file should be comma delimited, and the first line need to be the chromosome names of each bin

cleaned.binned.counts.fname

file name to write to for the corrected binned counts, default is not to write to file

gcContentFile

file name of a Rdata object with the gcContent data

gcCorrect

whether to do gc correction or not (True = do the correction)

PCA

whether to do PCA correction or not (True = do the correction)