#' generate wiggle tracks for HMMcopy
#'
#' @param sampleID the bam files
#' @param projName the project
#' @param location of bam files
#'
#' @export
genCNVmapGC <- function(projName,remRoot="/scratch/pschofield/Projects",
outPath="Analysis/wigs", noSub=F,ncores=1,scpIt=T,mem="16Gb",windowSize,
chrNames=c(seq(1,22),"X","Y"),genomeFasta, mapFile,
hmmCopyMod= "apps/hmmcopy/0.99.0/gcc-4.4.7"){
outDir=file.path(remRoot,projName,outPath)
script <- c(
paste0("mkdir -p ",outDir),
paste0("module load ",hmmCopyMod),
paste0("gcCounter -w ",windowSize," -c ",paste0(chrNames,collapse=",")," ", genomeFasta,
" > ",file.path(outDir,paste0("/GC_w",windowSize,".wig"))),
paste0("mapCounter -w ",windowSize, " -c ", paste0("chr",chrNames,collapse=",")," ", mapFile,
" > ", file.path(outDir,paste0("DukeMappability35mer_w",windowSize,".wig")))
)
plib::runScript(jname=paste0("gengcmap_"),jproj=projName,
jdesc=paste0("generate HMMCopy wig for project ",projName ),
jscrp=script,noSub=noSub,nproc=ncores,scpIt=scpIt,mem="32Gb")
}
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