scoreSequence: Score observations

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function computes the per-position and per-strand score in a given DNA sequence.

Usage

scoreSequence(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

fscores

Vector of scores on the forward strand

rscores

Vector of scores on the reverse 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
scoreSequence(seqs[[1]], motif, bg)

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