score_sequences: Score Sequences with PWM

In transite: RNA-binding protein motif analysis

Description

C++ implementation of PWM scoring algorithm

Usage

score_sequences(sequences, pwm)

Arguments

sequences	list of sequences
pwm	position weight matrix

Value

list of PWM scores for each sequence

Examples

motif <- get_motif_by_id("M178_0.6")[[1]]
sequences <- c("CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU",
               "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
               "AUCAAAUUA", "UGUGGGG", "GACACUUAAAGAUCCU",
               "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA", "AUAGAC",
               "AGUUC", "CCAGUAA")
seq_char_vectors <- lapply(sequences, function(seq) {
  unlist(strsplit(seq, ""))
})
score_sequences(seq_char_vectors, as.matrix(get_motif_matrix(motif)))

transite documentation built on Nov. 8, 2020, 5:27 p.m.