motifHitProfile {motifcounter} | R Documentation |
This function computes the per-position average motif hit profile across a set of fixed-length DNA sequences. It can be used to reveal positional constraints of TFBSs.
motifHitProfile(seqs, pfm, bg)
seqs |
A DNAStringSet object |
pfm |
An R matrix that represents a position frequency matrix |
bg |
A Background object |
List containing
Per-position average forward strand motif hits
Per-position average reverse strand motif hits
# Load sequences seqfile = system.file("extdata", "seq.fasta", package = "motifcounter") seqs = Biostrings::readDNAStringSet(seqfile) seqs = seqs[1:10] # 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 motif hit profile motifHitProfile(seqs, motif, bg)