VLF (version 1.1)

aa.find.singles: Find amino acid singles

Description

Determines the number of shared and singleton amino acid VLFs.

Usage

aa.find.singles(aaSpecies, seqlength)

Value

A matrix containing the number of singleton and shared aaVLFs in each position of the barcode.

Arguments

aaSpecies

List of amino acid sequences separated by species name.

seqlength

Length of amino acid sequences.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument aaSpecies contains only amino acid VLFs, and NAs in any other position in the sequence. The list can be created using the separate function.

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_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)
birds_aaVLFreduced <- aa.VLF.reduced(birds_aminoAcidVLFs, birds_aminoAcid_specimenVLFcount, 216)
birds_aaSpecies <- separate(birds_aaVLFreduced)
birds_aminoAcid_singleAndShared <- aa.find.singles(birds_aaSpecies, 216)