compoundPoissonDist: Compound Poisson Approximation

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function approximates the distribution of the number of motif hits that emerges from a random DNA sequence of a given length.

Usage

compoundPoissonDist(seqlen, overlap, method = "kopp")

Arguments

seqlen	Integer-valued vector that defines the lengths of the individual sequences. For a given DNAStringSet, this information can be retrieved using numMotifHits.
overlap	An Overlap object.
method	String that defines which method shall be invoked: 'pape' or 'kopp' (see description). Default: method = 'kopp'.

Details

The distribution can be determined in two alternative ways:

1. A re-implemented version of the algorithm that was described in Pape et al. Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands. 2008 can be invoked using method='pape'. The main purpose of this implementation concerns benchmarking an improved approximation. In contrast to the original model, this implementation can be used with general order-d Markov models.

2. We provide an improved compound Poisson approximation that uses more appropriate statistical assumptions concerning overlapping motif hits and that can be used with order-d background models as well. The improved version is used by default with method='kopp'. Note: Only method='kopp' supports the computation of the distribution of the number of motif hits w.r.t. scanning a single DNA strand (see probOverlapHit).

Value

List containing

dist

Distribution of the number of hits

See Also

combinatorialDist

probOverlapHit

numMotifHits

Examples

# Load sequences
seqfile = system.file("extdata", "seq.fasta", package = "motifcounter")
seqs = Biostrings::readDNAStringSet(seqfile)

# Load motif
motiffile = system.file("extdata", "x31.tab", package = "motifcounter")
motif = t(as.matrix(read.table(motiffile)))

# Load background model
bg = readBackground(seqs, 1)

# Use 100 individual sequences of length 150 bp each
seqlen = rep(150, 100)

# Compute overlapping probabilities
# for scanning the forward DNA strand only
op = motifcounter:::probOverlapHit(motif, bg, singlestranded = TRUE)

# Computes  the compound Poisson distribution
dist = motifcounter:::compoundPoissonDist(seqlen, op)
#plot(1:length(dist$dist)-1, dist$dist)

# Compute overlapping probabilities
# for scanning the forward DNA strand only
op = motifcounter:::probOverlapHit(motif, bg, singlestranded = FALSE)

# Computes  the compound Poisson distribution
dist = motifcounter:::compoundPoissonDist(seqlen, op)
#plot(1:length(dist$dist)-1, dist$dist)

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