fragCounter: fragCounter

In mskilab/fragCounter: GC mappability correction and segmentation

fragCounter

Description

Runs entire fragCounter pipeline

Usage

fragCounter(
  bam,
  skeleton,
  cov = NULL,
  midpoint = TRUE,
  window = 200,
  gc.rds.dir,
  map.rds.dir,
  minmapq = 1,
  reference = NULL,
  paired = TRUE,
  outdir = NULL,
  exome = FALSE,
  use.skel = FALSE,
  chr.sub = TRUE
)

Arguments

bam	string path to .bam or .cram file
skeleton	string Input data.table with intervals for which there is coverage data
cov	string path to existing coverage rds or bedgraph
midpoint	boolean If TRUE only count midpoint if FALSE then count bin footprint of every fragment interval
window	integer window / bin size
gc.rds.dir	string for tiles of width W, will look here for a file named gcW.rds in this directory
map.rds.dir	string for tiles of width W will look here for a file named mapW.rds in this directory
minmapq	double Minimal map quality
reference	reference file (recommended for CRAM, [NULL]
paired	boolean wether or not paired
outdir	string Directory to dump output into
exome	boolean If TRUE, perform correction using exons as bins instead of fixed size
use.skel	boolean flag If false then default exome skeleton from gencode is used, if TRUE, user defined skeleton is usde
chr.sub	boolean if TRUE, remove 'chr' prefix on seqnames. default TRUE

Author(s)

Marcin Imielinski

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