scoreSequences {transite}R Documentation

Score Sequences with PWM

Description

C++ implementation of PWM scoring algorithm

Usage

scoreSequences(sequences, pwm)

Arguments

sequences

list of sequences

pwm

position weight matrix

Value

list of PWM scores for each sequence

Examples

motif <- getMotifById("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, ""))
})
scoreSequences(seq.char.vectors, as.matrix(motifMatrix(motif)))
[Package transite version 1.5.0 Index]