VLF (version 1.1)

VLF.convert.matrix: VLF Matrix Convert

Description

Converts a matrix of nucleotide frequencies for each specimen into a matrix consisting entirely of very low frequency variant (VLF) frequencies and NAs in each other position.

Usage

VLF.convert.matrix(seq.matrix, freq, p, seqlength)

Value

A matrix of VLF nucleotide frequencies, containing only those nucleotide frequencies that occur less than the designation p value, and NAs in each other position of the matrix.

Arguments

seq.matrix

A matrix of aligned DNA barcode sequences.

freq

A matrix of nucleotide frequencies for each specimen.

p

A very low frequency variant designation cut off frequency. Any frequency in the freq matrix below this value is considered to be a very low frequency variant.

seqlength

Length of nucleotide sequence.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument freq can be calculated using the function specimen.frequencies.

Examples

if (FALSE) data(birds_aminoAcids)
birds_aminoAcid_speciesNames <- birds_aminoAcids[,2]
aminoAcids_specimenNumber <- nrow(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
bird_aminoAcid_frequencies <- aa.specimen.frequencies(aminoAcid_frequency.Matrix, birds_aminoAcids,
    birds_aminoAcid_speciesNames, 216)
aminoAcid_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
birds_aminoAcid_specimenVLFcount <- aa.VLF.count.spec(bird_aminoAcid_frequencies, 0.001, 216)
birds_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aminoAcid_frequencies,0.001,216)