Kmers processing.

split_to_kmers(.data, .k)

kmer_profile(.data, .method = c("freq", "prob", "wei", "self"), .remove.stop = T)

Arguments

.data

Character vector or the output from getKmers.

.k

Integer. Size of kmers.

.method

Character vector of length one. If "freq" then return a position frequency matrix (PFM) - a matrix with occurences of each amino acid in each position.

If "prob" then return a position probability matrix (PPM) - a matrix with probabilities of occurences of each amino acid in each position. This is a traditional representation of sequence motifs.

If "wei" then return a position weight matrix (PWM) - a matrix with log likelihoods of PPM elements.

If "self" then return a matrix with self-information of elements in PWM.

For more information see https://en.wikipedia.org/wiki/Position_weight_matrix.

.remove.stop

Logical. If TRUE (by default) remove stop codons.

Value

split_to_kmers - Data frame with two columns (kmers and their counts).

kmer_profile - a matrix with per-position amino acid statistics.