scoreThreshold {motifcounter} | R Documentation |
This function computes the score threshold for a desired false positive probability 'alpha'.
scoreThreshold(pfm, bg)
pfm |
An R matrix that represents a position frequency matrix |
bg |
A Background object |
Note that the returned alpha usually differs slightly
from the one that is prescribed using
motifcounterOptions
, because
of the discrete nature of the sequences.
List containing
Score threshold
False positive probability
# 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 threshold motifcounter:::scoreThreshold(motif, bg)