genCNVwigs: generate wiggle tracks for HMMcopy

Description Usage Arguments

View source: R/genCNVwigs.R

Description

generate wiggle tracks for HMMcopy

Usage

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genCNVwigs(sampleID, projName, bamDir, bamExt = "_dedup_realn_recal.bam",
  outDir = file.path("/scratch/pschofield/Projects", projName,
  "Analysis/wigs"), noSub = T, ncores = 1, scpIt = T, mem = "16Gb",
  windowSize, chrNames = c(seq(1, 22), "X", "Y"),
  hmmCopyMod = "apps/hmmcopy/0.99.0/gcc-4.4.7")

Arguments

sampleID

the bam files

projName

the project

location

of bam files


PietaSchofield/plibb documentation built on Nov. 11, 2018, 5:15 a.m.