VLF.aminoAcids: Amino Acid VLFs

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

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)

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.

Details

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

Value

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

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)
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)
## End(Not run)

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