VLF (version 1.1)

aa.VLF.reduced: Amino Acid Reduced

Description

Reduces a matrix of amino acid very low frequency variants (aaVLFs) so that only those specimen that contain aaVLFs remain

Usage

aa.VLF.reduced(NA.matrix, sCount, seqlength)

Value

A matrix containing only specimen with aaVLFs, and only the aaVLF values in the sequences. All other positions of the sequence contain NAs.

Arguments

NA.matrix

A matrix with values for amino acid very low frequency variants for each specimen and NAs in all other positions.

sCount

A vector for amino acid very low frequency variant (VLF) counts for each specimen in the NA.matrix.

seqlength

Length of the amino acid sequences.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument NA.matrix can be calculated using aa.VLF.convert.matrix and VLF.aminoAcids, the sCount argument can be calculaed using the aa.VLF.count.spec 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)