read_targets — read_targets • breakinspectoR

Read in a bed file with positions of breaks

Usage

read_targets(x, genome, standard_chromosomes, strandless)

Arguments

x: GRanges object with coordinates of breaks or the path to a bed file.
genome: a BSgenome object.
standard_chromosomes: logical, constrain the analysis to standard chromosomes only (defaults to TRUE).
strandless: collapse reads from multiple strands.

Value

A GRanges object, unstranded and with a `score` column

Examples

breaks <- read_targets(x=system.file("extdata/vegfa.chr6.bed.gz", package="breakinspectoR"),
                       genome="BSgenome.Hsapiens.UCSC.hg38",
                       standard_chromosomes=TRUE,
                       strandless=FALSE)