Count the k-mers of the accessible genome

The background depends on the regions only, so it is counted once and handed to computeKmerBias for every sample.

Usage

kmerBackground(regions, genome, k = 6L, chunk = 5000)

Arguments

regions

A GRanges of the accessible regions.

genome

A BSgenome object.

k

Length of the k-mer.

chunk

Number of regions read from the genome at a time.

Value

A named numeric vector of k-mer counts.

Examples

if (FALSE) { # \dontrun{
bg <- kmerBackground(peaks, BSgenome.Hsapiens.UCSC.hg38::Hsapiens)
} # }