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adding chip label column to awk output #27

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adding chip label column to awk output #27

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2 changes: 1 addition & 1 deletion Imp_Scripts/DiffAnalysisHiChIP.r
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Expand Up @@ -491,7 +491,7 @@ FillFeatureValues <- function(UnionLoopFile, AllLoopList, BinSize, ChIPCovFileLi
# check the first field of chromosome name
# and second and third fields as integers
# extract the bin number and the coverage information (assume 4th field)
system(paste0("awk -v b=", BinSize, " \'{if (($1==\"", chrName, "\") && ($2 ~ /^[0-9]+$/) && ($3 ~ /^[0-9]+$/)) {print ($2/b)\"\t\"$4}}\' ", currcovfile, " > ", InpTempChIPCoverageFile))
system(paste0("awk -v b=", BinSize, " \'{if (($1==\"", chrName, "\") && ($2 ~ /^[0-9]+$/) && ($3 ~ /^[0-9]+$/)) {print ($2/b)\"\t\"$4\"\t\"$5}}\' ", currcovfile, " > ", InpTempChIPCoverageFile))

# read the ChIP coverage for the current sample and for the current chromosome
# ChIPCoverageData <- read.table(InpTempChIPCoverageFile, header=F, sep="\t", stringsAsFactors=F)
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