R: Empirical score distribution

scoreDistEmpirical {motifcounter}

R Documentation

Empirical score distribution

Description

This function estimates the empirical score distribution on a set of randomly generated DNA sequences based on the background model. This function is only used for benchmarking analysis.

Usage

scoreDistEmpirical(pfm, bg, seqlen, nsim)

Arguments

`pfm`	An R matrix that represents a position frequency matrix
`bg`	A Background object
`seqlen`	Integer-valued vector that defines the lengths of the individual sequences. For a given DNAStringSet, this information can be retrieved using `numMotifHits`.
`nsim`	Integer number of random samples.

Value

List containing

scores: Vector of scores
dist: Score distribution

Examples


# 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)))


# Compoute the empirical score distribution in
# sequences of length 1kb using 1000 samples
motifcounter:::scoreDistEmpirical(motif, bg, seqlen = 1000, nsim = 1000)