calcGCContentRef: Calculate GC content over genomic ranges

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Calculate GC content over genomic ranges

Description

Given a reference genome as a BSgenome object and some ranges on that reference, this function will return a vector of the same length as the granges object, with percent of Cs and Gs.

Usage

calcGCContentRef(query, refAssembly)

Arguments

query	A GenomicRanges or GenomicRangesList object with query regions
refAssembly	A character vector specifying the reference genome assembly (*e.g.* 'hg19'). This will be used to grab chromosome sizes with getTSSs.

Value

A numeric vector or list of vectors with the GC percentage of the query regions.

Examples

## Not run: 
refAssembly = 'hg19'
GCcontent = calcGCContentRef(vistaEnhancers, refAssembly)

## End(Not run) 

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.