CleanBEDtoBG: CleanBEDtoBG

In vbusa1/nearBynding: Discern RNA structure proximal to protein binding

Description

Writes a script to convert a BED file to a clean bedGraph file.

Usage

CleanBEDtoBG(
  in_bed,
  out_bedGraph = NA,
  unwanted_chromosomes = NULL,
  alignment = "hg19"
)

Arguments

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"

Value

deposits bedGraph from BED in same directory

Examples

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")

vbusa1/nearBynding documentation built on Aug. 4, 2021, 4:08 p.m.