#' generate some bigwig tracks from paired reads
#'
#' @param projName project name
#' @param fileList bam files to use
#' @param outPath directory to write output to
#'
#' @export
genCovTracks <- function(projName,fileList, outPath, paired=T){
outDir <- file.path("/scratch/pschofield/Projects",projName,outPath)
lapply(fileList,function(ffn){
fname <- basename(ffn)
bamDir <- dirname(ffn)
fn <- gsub("[.]bam$","",fname)
if(paired){
rline <- paste0("frags <- readGAlignmentPairs('",file.path(bamDir,fname),"')")
}else{
rline <- paste0("frags <- readGAlignments('",file.path(bamDir,fname),"')")
}
rscript <- c(
"require(GenomicAlignments)",
"require(rtracklayer)",
rline,
"covTrack <- coverage(frags)",
paste0("dir.create('",outDir,"',recursive=T,showWarnings=F)"),
paste0("export(covTrack,con='",file.path(outDir,gsub("bam$","bw",fname)),"')"),
"q()"
)
plib::runRScript(rscript,jname=paste0("bam2bw_",fn),jproj=projName,
jdesc=paste0("Run Rscript to make bw ",fname," "))
})
}
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