CleanBEDtoBG {nearBynding} | R Documentation |
Writes a script to convert a BED file to a clean bedGraph file.
CleanBEDtoBG( in_bed, out_bedGraph = NA, unwanted_chromosomes = NULL, alignment = "hg19" )
in_bed |
Name of sorted BAM file to be converted to a bedGraph file. Required. |
out_bedGraph |
Name of bedGraph output file, including full directory path; a string. Default in_bam prefix. |
unwanted_chromosomes |
A vector of unwanted chromosomes that are present in the BAM file. |
alignment |
The human genome alignment used, either "hg19" or "hg38". Default "hg19" |
deposits bedGraph from BED in same directory
bam <- system.file("extdata/chr4and5.bam", package="nearBynding") out_bed <- "bamto.bed" ## convert BAM to BED if(suppressWarnings(system2("bedtools", "--version", stdout = NULL, stderr = NULL)) == 0){ system2("bedtools", paste0("bamtobed -i ", bam, " > ", out_bed)) } CleanBEDtoBG(in_bed = out_bed, alignment = "hg38")