scoreHistogramSingleSeq {motifcounter}R Documentation

Score histogram on a single sequence

Description

This function computes the empirical score distribution by normalizing the observed score histogram for a given sequence.

Usage

scoreHistogramSingleSeq(seq, pfm, bg)

Arguments

seq

A DNAString object

pfm

An R matrix that represents a position frequency matrix

bg

A Background object

Value

List containing

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 per-position and per-strand scores
motifcounter:::scoreHistogramSingleSeq(seqs[[1]], motif, bg)


[Package motifcounter version 1.18.0 Index]