clumpSizeDist: Clump size distribution

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function approximates the distribution of the clump sizes.

Usage

clumpSizeDist(maxclump, overlap, method = "kopp")

Arguments

maxclump	Maximal clump size
overlap	An Overlap object.
method	String that defines which method shall be invoked: 'pape' or 'kopp' (see description). Default: method = 'kopp'.

Details

The clump size 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'.

2. An improved approximation of the clump size distribution 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'.

Value

List containing

dist

Distribution of the clump size

See Also

probOverlapHit

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 = FALSE)

# Computes  the compound Poisson distribution
dist = motifcounter:::clumpSizeDist(20, op)

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