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 1.2.1 Index]