scoreDist: Score distribution

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function computes the score distribution for the given PFM and background. The Score distribution is computed based on an efficient dynamic programming algorithm.

Usage

scoreDist(pfm, bg)

Arguments

pfm	An R matrix that represents a position frequency matrix
bg	A Background object

Value

List that contains

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)))

# Compute the score distribution
dp = scoreDist(motif, bg)

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