VLF (version 1.1)

aa.VLF.convert.matrix: Convert Amino Acid Matrix

Description

Converts a matrix of amino acid frequencies for each specimen into a matrix consisting of only VLF values and NAs in every non-VLF position.

Usage

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

Value

A matrix of VLF amino acid 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 amino acid sequences.

freq

A matrix of amino acid frequencies for each specimen.

p

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

seqlength

The length of the amino acid sequences.

Author

Taryn B. T. Athey and Paul D. McNicholas

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)
birds_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aminoAcid_frequencies, 0.001, 
    216)