scoreSequence {motifcounter} | R Documentation |
This function computes the per-position and per-strand score in a given DNA sequence.
scoreSequence(seq, pfm, bg)
seq |
A DNAString object |
pfm |
An R matrix that represents a position frequency matrix |
bg |
A Background object |
List containing
Vector of scores on the forward strand
Vector of scores on the reverse strand
# Load sequences seqfile = system.file("extdata", "seq.fasta", package = "motifcounter") seqs = Biostrings::readDNAStringSet(seqfile) # Load background bg = readBackground(seqs, 1) # Load motif motiffile = system.file("extdata", "x31.tab", package = "motifcounter") motif = t(as.matrix(read.table(motiffile))) # Compute the per-position and per-strand scores scoreSequence(seqs[[1]], motif, bg)