scoreDistBf {motifcounter} | R Documentation |
This function computes the score distribution for a given PFM and a background model.
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
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 score distribution dp = motifcounter:::scoreDistBf(motif, bg)