motifHitProfile {motifcounter}R Documentation

Motif hit profile across multiple sequences

Description

This function computes the per-position average motif hit profile across a set of fixed-length DNA sequences. It can be used to reveal positional constraints of TFBSs.

Usage

motifHitProfile(seqs, pfm, bg)

Arguments

seqs

A DNAStringSet object

pfm

An R matrix that represents a position frequency matrix

bg

A Background object

Value

List containing

fscores

Per-position average forward strand motif hits

rscores

Per-position average reverse strand motif hits

Examples




# Load sequences
seqfile = system.file("extdata", "seq.fasta", package = "motifcounter")
seqs = Biostrings::readDNAStringSet(seqfile)
seqs = seqs[1:10]

# 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 motif hit profile
motifHitProfile(seqs, motif, bg)


[Package motifcounter version 1.4.0 Index]