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