aa.VLF.reduced: Amino Acid Reduced

In VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

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)

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.

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.

Value

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

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
## End(Not run)

VLF documentation built on April 12, 2025, 1:22 a.m.