regionCounts: Get regional counts for given GRanges or GRangesList object

In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

Convert methylRaw, methylRawList or methylBase object into regional counts for a given GRanges or GRangesList object.

Usage

  regionCounts(object,regions,cov.bases=0,strand.aware=FALSE)

Arguments

object	a methylRaw or methlRawList object
regions	a GRanges or GRangesList object.
cov.bases	number minimum bases covered per region (Default:0). Only regions with base coverage above this threshold are returned.
strand.aware	if set to TRUE only CpGs that match the strand of the region will be summarized. (default:FALSE)

Value

a new methylRaw,methylBase or methylRawList object. If strand.aware is set to FALSE (default). Even though the resulting object will have the strand information of regions it will still contain methylation information from both strands.

Examples

data(methylKit)

# get the windows of interest as a GRanges object, this can be any set
# of genomic locations
library(GenomicRanges)
my.win=GRanges(seqnames="chr21",
ranges=IRanges(start=seq(from=9764513,by=10000,length.out=20),width=5000) )

# getting counts per region
regional.methylRaw=regionCounts(object=methylRawList.obj, regions=my.win,
cov.bases=0,strand.aware=FALSE)

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.