scoreDistEmpirical: Empirical score distribution

In motifcounter: R package for analysing TFBSs in DNA sequences

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

See Also

scoreDist

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)

motifcounter documentation built on Nov. 8, 2020, 5:44 p.m.