gc: GC Content

Description Usage Arguments Value Examples

Description

Compute the GC content for regions of a reference sequence.

Usage

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  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

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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. 1, 2018, 2:23 a.m.