motifAndBackgroundValid: Check valididity of PFM with background

In motifcounter: R package for analysing TFBSs in DNA sequences

Description

This function checks if the PFM x background combination is valid. The function throws an error if this is not the case.

Usage

motifAndBackgroundValid(pfm, bg)

Arguments

pfm	An R matrix that represents a position frequency matrix
bg	A Background object

Value

None

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", "x1.tab", package = "motifcounter")
motif = t(as.matrix(read.table(motiffile)))

# Check validity
motifcounter:::motifAndBackgroundValid(motif, bg)

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