keepRelevantChrs: keepRelevantChrs

In DEScan2: Differential Enrichment Scan 2

Description

subselect a list of GRanges created with cutGRangesPerChromosome returning only the relevant chromosomes GRanges.

Usage

keepRelevantChrs(chrGRangesList, chr = NULL)

Arguments

chrGRangesList	where each element is a chromosome, tipically created with cutGRangesPerChromosome.
chr	a character vector of chromosomes names of the form "chr#".

Value

the input chrGRangesList with only the relevat chromosomes.

Examples

library("GenomicRanges")
gr1 <- GRanges(
            seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
            ranges=IRanges(1:10, end=10),
            strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
            seqlengths=c(chr1=11, chr2=12, chr3=13))
grlc <- cutGRangesPerChromosome(gr1)
(grlChr <- keepRelevantChrs(grlc, c("chr1", "chr3")))

DEScan2 documentation built on Nov. 8, 2020, 5:01 p.m.