motifHits: Motif hit observations

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

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

Usage

motifHits(seq, pfm, bg, threshold = NULL)

Arguments

seq	A DNAString object
pfm	An R matrix that represents a position frequency matrix
bg	A Background object
threshold	Score threshold for calling motif matches. If NULL, the threshold will determined from alpha.

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)

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