VLF (version 1.1)

VLF.aminoAcids: Amino Acid VLFs

Description

Converts a matrix of amino acid frequencies into a matrix of amino acids.

Usage

VLF.aminoAcids(convert.matrix, seq.matrix, seqlength)

Value

A matrix containing only aaVLFs and NAs in every other position of the sequence.

Arguments

convert.matrix

A matrix consisting of only aaVLF frequencies for each specimen, and NAs in every other position of the sequence.

seq.matrix

A matrix of amino acid sequences.

seqlength

The length of the amino acid sequence.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument convert.matrix can be calculated using the function aa.VLF.convert.matrix

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)
birds_aminoAcidVLFs <- VLF.aminoAcids(birds_aaVLFconvert, birds_aminoAcids, 216)