CleanBEDtoBG: CleanBEDtoBG
In nearBynding: Discern RNA structure proximal to protein binding

Description Usage Arguments Value Examples

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")