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

Description Usage Arguments Value

View source: R/utility.r

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

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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.