calcDinuclFreqRef {GenomicDistributions} | R 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)

[Package GenomicDistributions version 1.2.0 Index]