Bam2FragCounts: Import bam files and generate read counts per GATC fragment

In lpagie/chromocounting: Compute OE Scores for Chromocount Experiments

Description

BamToFragCounts generates read counts per GATC fragment for a set of bam files.

Usage

Bam2FragCounts(meta.data, bam.dir, GATC.fragments, maxgap = 0, shift = 0,
  VERBOSE = FALSE, addToName = "")

Arguments

meta.data	Data frame.
bam.dir	Character, directory which contains the bamfiles.
GATC.fragments	GRanges object with GATC regions.
maxgap	Integer, maximum allowed gap between read alignment position and GATC position.
shift	Integer, exact number of bases by which reads are shifted before comparing to GATC position.
VERBOSE	Logical, print diagnostic msgs [default = FALSE].
addToName	Character, string which is added to the chromosome names read from the bamfile

Details

extended description of function

Value

GRanges object; granges specify genomic GATC fragments, mcols specify readcounts (forw/rev/both) per sample

lpagie/chromocounting documentation built on May 21, 2019, 2:26 a.m.