calcDinuclFreqRef: Calculate dinucleotide content over genomic ranges

View source: R/content-plots.R

calcDinuclFreqRefR Documentation

Calculate dinucleotide content over genomic ranges

Description

Given a reference genome (BSgenome object) and ranges on the reference, this function returns a data.table with counts of dinucleotides within the GRanges object.

Usage

calcDinuclFreqRef(query, refAssembly, rawCounts = FALSE)

Arguments

query

A GRanges object with query sets

refAssembly

A character vector specifying the reference genome assembly (*e.g.* 'hg19'). This will be used to grab chromosome sizes with getTSSs.

rawCounts

a logical indicating whether the raw numbers should be displayed, rather than percentages (optional).

Value

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

Examples

## Not run: 
query = system.file("extdata", "vistaEnhancers.bed.gz", package="GenomicDistributions")
GRquery = rtracklayer::import(query)
refAssembly = 'hg19'
DNF = calcDinuclFreqRef(GRquery, refAssembly)

## End(Not run) 

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