motifHits {motifcounter}R Documentation

Motif hit observations

Description

This function determines per-position motif hits in a given DNA sequence.

Usage

motifHits(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

fhits

Per-position motif hits on the forward strand

rhits

Per-position motif hits on the reverse strand

Examples



# Load sequences
seqfile = system.file("extdata", "seq.fasta", package = "motifcounter")
seq = Biostrings::readDNAStringSet(seqfile)

# Load background
bg = readBackground(seq, 1)

# Load motif
motiffile = system.file("extdata", "x31.tab", package = "motifcounter")
motif = t(as.matrix(read.table(motiffile)))

# Determine the motif hits
motifHits(seq[[1]], motif, bg)


[Package motifcounter version 1.4.0 Index]