scan_genomic_bedpe: Scan genomic BEDPE

In trichelab/spiky: Spike-in calibration for cell-free MeDIP

Scan genomic BEDPE

Description

Scan genomic BEDPE

Usage

scan_genomic_bedpe(
  bedpe,
  bin = TRUE,
  binwidth = 300L,
  bins = NULL,
  standard = TRUE,
  genome = "hg38"
)

Arguments

bedpe	the BEDPE file path, or output from read_bedpe()
bin	Bin reads? (TRUE)
binwidth	width of the bins for chromosomal tiling (300)
bins	a pre-tiled GRanges for binning coverage (NULL)
standard	restrict non-spike contigs to "standard" chromosomes? (TRUE)
genome	Name of genome (default hg38)

Value

     a GRanges with coverage

Examples

fl <- system.file("extdata", "example_chr21_bedpe.bed.gz", package="spiky",mustWork=TRUE)
scan_genomic_bedpe(fl) # will warn user about spike contigs

trichelab/spiky documentation built on Sept. 17, 2022, 8:44 a.m.