setGRGenomeInfo: setGRGenomeInfo given a genome code (i.e....

In DEScan2: Differential Enrichment Scan 2

Description

setGRGenomeInfo given a genome code (i.e. "mm9","mm10","hg19","hg38") retrieve the SeqInfo of that genome and assigns it to the input GRanges. Finally filters out those Infos not necessary to the GRanges.

Usage

setGRGenomeInfo(GRanges, genomeName = NULL, verbose = FALSE)

Arguments

GRanges	a GRanges object.
genomeName	a genome code (i.e. "mm9")
verbose	verbose output

Value

a GRanges object with the seqinfo of the genome code

Examples

library("GenomicRanges")
gr <- 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))
mm9gr <- setGRGenomeInfo(GRanges=gr, genomeName="mm9", verbose=TRUE)

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