scoreDistBf: Score distribution
In motifcounter: R package for analysing TFBSs in DNA sequences

Description Usage Arguments Details Value See Also Examples

This function computes the score distribution for a given PFM and a background model.

1	scoreDistBf(pfm, bg)

`pfm`	An R matrix that represents a position frequency matrix
`bg`	A Background object

The result of this function is identical to scoreDist, however, the method employs a less efficient algorithm that enumerates all DNA sequences of the length of the motif. This function is only used for debugging and testing purposes and might require substantial computational resources for long motifs.

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 score distribution
dp = motifcounter:::scoreDistBf(motif, bg)