aa.compare: Amino Acid Comparison

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

Amino Acid Comparison

Description

Compares amino acid very low frequency variants between specimen of the same species

Usage

aa.compare(x, seqlength)

Arguments

x	A list of amino acid sequences separated by species name.
seqlength	The length of the amino acid sequences within the list.

Details

The argument x can be calculated using the separate function.

Value

A matrix containing two vectors, one with singleton VLF counts for each position of the sequence, and one with shared VLF counts for each 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)
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.