Calculate dinucleotide content over genomic ranges

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.

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

if (FALSE) { # \dontrun{
query = system.file("extdata", "vistaEnhancers.bed.gz", package="GenomicDistributions")
GRquery = rtracklayer::import(query)
refAssembly = 'hg19'
DNF = calcDinuclFreqRef(GRquery, refAssembly)
} # }