k-mer identities along a set of binding sites

The sequence is read once and reused for every sample, so fitting the Tn5 model per sample costs a table lookup rather than a second pass over the genome.

Usage

kmerIndexProfile(tfbs, genome, kmers, k = 6L, max.sites = 25000)

Arguments

tfbs

A GRanges of binding sites, prepared with prepareTFBS.

genome

A BSgenome object.

kmers

The k-mer vocabulary, the names of a bias vector.

k

Length of the k-mer.

max.sites

Number of binding sites drawn for the estimate.

Value

A list with the offsets x and the index matrix idx of sites by positions.

Examples

if (FALSE) { # \dontrun{
prof <- kmerIndexProfile(tfbs, Hsapiens, names(bias))
} # }