| scoreHistogram {motifcounter} | R Documentation |
This function computes the empirical score distribution for a given set of DNA sequences.
scoreHistogram(seqs, pfm, bg)
seqs |
A DNAStringSet or DNAString object |
pfm |
An R matrix that represents a position frequency matrix |
bg |
A Background object |
It can be used to compare the empirical score
distribution against the theoretical one (see scoreDist).
List containing
Vector of scores
Score distribution
# 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 empirical score histogram
scoreHistogram(seqs, motif, bg)