| motifHits {motifcounter} | R Documentation |
This function determines per-position motif hits in a given DNA sequence.
motifHits(seq, pfm, bg, threshold = NULL)
seq |
A DNAString object |
pfm |
An R matrix that represents a position frequency matrix |
bg |
A Background object |
threshold |
Score threshold for calling motif matches. If NULL, the threshold will determined from alpha. |
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)