aa.find.singles: Find amino acid singles

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

Find amino acid singles

Description

Determines the number of shared and singleton amino acid VLFs.

Usage

aa.find.singles(aaSpecies, seqlength)

Arguments

aaSpecies	List of amino acid sequences separated by species name.
seqlength	Length of amino acid sequences.

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.

Value

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

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)
birds_aaSpecies <- separate(birds_aaVLFreduced)
birds_aminoAcid_singleAndShared <- aa.find.singles(birds_aaSpecies, 216)
## End(Not run)

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