scoreSequences {transite} | R Documentation |
C++ implementation of PWM scoring algorithm
scoreSequences(sequences, pwm)
sequences |
list of sequences |
pwm |
position weight matrix |
list of PWM scores for each sequence
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)))