filterByCov: Filters regions (or single CpGs) of a 'BSraw' object with a...

In BiSeq: Processing and analyzing bisulfite sequencing data

Description

This method reduces a BSraw object to its regions (or single CpGs) with a minimum number of reads.

Usage

filterByCov(object, minCov, global)

Arguments

object	A BSraw.
minCov	Minimum number of reads overlapping the CpG sites.
global	A logical indicating whether the regions should achieve the minimum coverage in each sample. If global = TRUE the filtered object will consist of the regions achieving the minimum coverage in all samples. If global = FALSE (default) this function filters the regions for each sample separately, irrespectively of the coverages in other samples. totalReads and methReads are set to zero, if the minimum coverage is not obtained. Regions covered too sparse in all samples are dropped.

Value

A BSraw object containing the CpGs or regions achieving the minimum coverage in all (if global=TRUE) or at least one (if global=FALSE) samples.

Author(s)

Katja Hebestreit

See Also

filterBySharedRegions

Examples

data(rrbs)
rrbs.reduced <- filterByCov(object=rrbs, minCov=10, global=TRUE)

BiSeq documentation built on Nov. 8, 2020, 8:05 p.m.