gc: GC Content

In SomaticSignatures: Somatic Signatures

Description

Compute the GC content for regions of a reference sequence.

Usage

  gcContent(regions, ref)

Arguments

regions	GRanges object with the regions for which the GC content should be computed.
ref	Reference sequence object, as a 'BSgenome' or 'FaFile' object.

Value

A numeric vector with the GC content [0,1] for each region.

Examples

library(BSgenome.Hsapiens.1000genomes.hs37d5)

regs = GRanges(c("1", "2"), IRanges(1e7, width = 100))

gc = gcContent(regs, BSgenome.Hsapiens.1000genomes.hs37d5)

SomaticSignatures documentation built on Nov. 8, 2020, 5:52 p.m.