aa.VLF.convert.matrix: Convert Amino Acid Matrix

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

Convert Amino Acid Matrix

Description

Converts a matrix of amino acid frequencies for each specimen into a matrix consisting of only VLF values and NAs in every non-VLF position.

Usage

aa.VLF.convert.matrix(seq.matrix, freq, p, seqlength)

Arguments

seq.matrix	A matrix of aligned DNA barcode amino acid sequences.
freq	A matrix of amino acid frequencies for each specimen.
p	A very low frequency variant cut-off frequency. Any frequency in the freq matrix below this value is considered to be a very low frequency variant.
seqlength	The length of the amino acid sequences.

Value

A matrix of VLF amino acid frequencies, containing only those nucleotide frequencies that occur less than the designation p value, and NAs in each other position of the matrix.

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_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aminoAcid_frequencies, 0.001, 
    216)
## End(Not run)

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