R: Score profile across multiple sequences

scoreProfile {motifcounter}

R Documentation

Score profile across multiple sequences

Description

This function computes the per-position and per-strand average score profiles across a set of DNA sequences. It can be used to reveal positional constraints of TFBSs.

Usage

scoreProfile(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: Vector of per-position average forward strand scores
rscores: Vector of per-position average reverse strand scores

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 score profile
scoreProfile(seqs, motif, bg)

[Package motifcounter version 1.6.0 Index]