split_to_kmers(.data, .k) kmer_profile(.data, .method = c("freq", "prob", "wei", "self"), .remove.stop = T)
Character vector or the output from
Integer. Size of kmers.
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.
Logical. If TRUE (by default) remove stop codons.
split_to_kmers - Data frame with two columns (kmers and their counts).
kmer_profile - a matrix with per-position amino acid statistics.