scoreHistogram {motifcounter}R Documentation

Score histogram

Description

This function computes the empirical score distribution for a given set of DNA sequences.

Usage

scoreHistogram(seqs, pfm, bg)

Arguments

seqs

A DNAStringSet or DNAString object

pfm

An R matrix that represents a position frequency matrix

bg

A Background object

Details

It can be used to compare the empirical score distribution against the theoretical one (see scoreDist).

Value

List containing

scores

Vector of scores

dist

Score distribution

See Also

scoreDist

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 empirical score histogram
scoreHistogram(seqs, motif, bg)


[Package motifcounter version 1.14.0 Index]