hitStrand: Hit strand

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function computes the per-position motif matches in a given DNA strand.

Usage

hitStrand(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.

Details

The function returns the per-position scores for the given strand. If the sequence is too short, it contains an empty vector.

Value

hits

Vector of motif hits on the given strand

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:::hitStrand(seqs[[1]], motif, bg)

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