PrepareCov: PrepareCov

In mskilab/fragCounter: GC mappability correction and segmentation

PrepareCov

Description

Load BAM or coverage file and prepare for use in correctcov_stub

Usage

PrepareCov(
  bam,
  skeleton,
  cov = NULL,
  reference = NULL,
  midpoint = TRUE,
  window = 200,
  minmapq = 1,
  paired = TRUE,
  outdir = NULL,
  exome = FALSE,
  use.skel = FALSE
)

Arguments

bam	path to .bam file
skeleton	string Input data.table with intervals for which there is coverage data
cov	Path to existing coverage rds or bedgraph
midpoint	If TRUE only count midpoint if FALSE then count bin footprint of every fragment interval
window	window / bin size
minmapq	Minimal map quality
paired	wether or not paired
outdir	Directory to dump output into
exome	boolean If TRUE, use bam.cov.exome to calculate coverage
use.skel	boolean flag If false then default exome skeleton from gencode is used, if TRUE, user defined skeleton is used

Author(s)

Marcin Imielinski

Trent Walradt

mskilab/fragCounter documentation built on Jan. 27, 2024, 2:35 p.m.