fromSamplesToChrsGRangesList: fromSamplesToChrsGRangesList

In drighelli/DEScan2: Differential Enrichment Scan 2

fromSamplesToChrsGRangesList

Description

converts a GRangesList orgnized per samples to a GRangesList organized per Chromosomes where each element is a GRangesList of samples.

Usage

fromSamplesToChrsGRangesList(samplesGRangesList)

Arguments

samplesGRangesList

a GRangesList of samples. Tipically generaed by findPeaks function.

Value

A GRangesList of chromosomes where each element is a GRanges list of samples.

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")
(chrGrlSampGr <- fromSamplesToChrsGRangesList(sgrl))

drighelli/DEScan2 documentation built on March 21, 2023, 3:06 p.m.