calcDinuclFreq: Calculate Dinuclotide content over genomic ranges

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

Calculate Dinuclotide 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

calcDinuclFreq(query, ref, rawCounts = FALSE)

Arguments

query	A GRanges object with query sets
ref	Reference genome BSgenome object
rawCounts	a logical indicating whether the raw numbers should be displayed, rather than percentages (optional).

Value

A data.table with counts of dinucleotides across the GRanges object

Examples

## Not run:  
bsg = loadBSgenome('hg19')
DNF = calcDinuclFreq(vistaEnhancers, bsg)

## End(Not run)

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