getCounts: Produce a GRanges with counts of overlapping reads for a set...

In jeffbhasin/methylaction: MethylAction: Differentially Methylated Regions (DMRs) from MBD-isolated Genome Sequencing (MiGS/MBD-seq)

Description

Compute counts in non-overlapping windows genome-wide on the chromosomes given in chrs and return as a GRanges object. The values() of the GRanges will contain a table of counts for each sample at each window.

Usage

getCounts(samp, reads, ranges = NULL, chrs = NULL, winsize = 50,
  ncore = 1)

Arguments

samp	Sample data.frame from readSampleInfo()
reads	Output from getReads()
ranges	Count within regions given by a GRanges object only
chrs	Character vector of chromosome names to select
winsize	Size of the non-overlapping windows
ncore	Number of parallel processes to use

Value

A GenomicRanges object with values() containing a table of counts for each sample at each window.

jeffbhasin/methylaction documentation built on May 19, 2019, 1:46 a.m.