scoreHistogram: Score histogram
In motifcounter: R package for analysing TFBSs in DNA sequences

Description Usage Arguments Details Value See Also Examples

This function computes the empirical score distribution for a given set of DNA sequences.

1	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

scores: Vector of scores
dist: Score distribution

scoreDist

# 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)