calcDinuclFreqRef {GenomicDistributions} | R Documentation |
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)
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
|
rawCounts |
a logical indicating whether the raw numbers should be displayed, rather than percentages (optional). |
A numeric vector or list of vectors with the GC percentage of the query regions.
## Not run: query = system.file("extdata", "vistaEnhancers.bed.gz", package="GenomicDistributions") GRquery = rtracklayer::import(query) refAssembly = 'hg19' DNF = calcDinuclFreqRef(GRquery, refAssembly) ## End(Not run)