simulateNumHitsDist: Empirical number of motif hits distribution

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function repeatedly simulates random DNA sequences according to the background model and subsequently counts how many motif hits occur in them. Thus, this function gives rise to the empirical distribution of the number of motif hits. This function is only used for benchmarking analysis.

Usage

simulateNumHitsDist(pfm, bg, seqlen, nsim, singlestranded = FALSE)

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.
singlestranded	Boolean that indicates whether a single strand or both strands shall be scanned for motif hits. Default: singlestranded = FALSE.

Value

A List that contains

dist

Empirical distribution of the number of motif hits

See Also

compoundPoissonDist,combinatorialDist

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)))

# Study the counts in one sequence of length 150 bp
seqlen = rep(150, 1)

# Compute empirical distribution of the number of motif hits
# by scanning both strands using 100 samples
simc = motifcounter:::simulateNumHitsDist(motif, bg,
    seqlen, nsim = 100, singlestranded = FALSE)

# Compute empirical distribution of the number of motif hits
# by scanning a single strand using 100 samples
simc = motifcounter:::simulateNumHitsDist(motif, bg,
    seqlen, nsim = 100, singlestranded = TRUE)

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