scoreDist {motifcounter}R Documentation

Score distribution

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)


[Package motifcounter version 1.10.0 Index]