divideEachSampleByChromosomes: divideEachSampleByChromosomes

In DEScan2: Differential Enrichment Scan 2

Description

taken in input a grangeslist of samples, generate a list of samples where each element has a GRangesList each element of the GRangesList represents a single chromosome.

Usage

divideEachSampleByChromosomes(samplesGRangesList)

Arguments

samplesGRangesList

a GRangesList of samples.

Value

list of samples where each element is a list of chromosomes and each of these elements is a GRanges.

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))
gr2 <- GRanges(
            seqnames=Rle(c("chr1", "chr4", "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, chr4=12, chr3=13))
sgrl <- GRangesList(gr1, gr2)
names(sgrl) <- c("samp1", "samp2")
(sampChrGrl <- divideEachSampleByChromosomes(sgrl))

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