scoreThreshold: Score threshold
In motifcounter: R package for analysing TFBSs in DNA sequences

Description Usage Arguments Details Value Examples

This function computes the score threshold for a desired false positive probability 'alpha'.

1	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

threshold: Score threshold
alpha: 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)