readBackground {motifcounter}R Documentation

Estimates a background model from a set of DNA sequences

Description

Given a set of DNA sequences and an order, this function estimates an order-d Markov model which is used to characterize random DNA sequences.

Usage

readBackground(seqs, order = 1)

Arguments

seqs

A DNAStringSet object

order

Order of the Markov models that shall be used as the background model. Default: order = 1.

Value

A Background object

Examples


# Load sequences
file = system.file("extdata", "seq.fasta", package = "motifcounter")
seqs = Biostrings::readDNAStringSet(file)

# Estimate an order-1 Markov model
bg = readBackground(seqs, 1)


[Package motifcounter version 1.14.0 Index]