motifHitProfile: Motif hit profile across multiple sequences

In motifcounter: R package for analysing TFBSs in DNA 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 or DNAString 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)

motifcounter documentation built on Nov. 8, 2020, 5:44 p.m.