aaVLFs.to.modalchanges: Amino Acid Changes

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

Amino Acid Changes

Description

Determines how many aaVLFs have changed “type” of amino acid from the modal amino acid sequence. Amino acid types are polar charged, polar uncharged, non-polar, and those with a unique side group.

Usage

aaVLFs.to.modalchanges(modal, AminoAcidList, aalength)

Arguments

modal	The modal amino acid sequence (i.e., the amino acid sequence that occurs most often based on the amino acid frequency matrix)
AminoAcidList	Matrix of VLF amino acid sequences containing only aaVLFs and NAs anywhere else
aalength	Amino Acid sequence length.

Details

The argument modal can be created using the MODE function. The argument AminoAcidList can be created using the aa.VLF.convert.matrix, VLF.aminoAcids, and aa.VLF.reduced functions.

Value

A sameAll value representative of the number of amino acids that were the same type as the modal, a changedAll value representative of the number of amino acids that changed amino acid type from the modal.

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)
birds_aaVLFreduced <- aa.VLF.reduced(birds_aminoAcidVLFs, birds_aminoAcid_specimenVLFcount, 216)
All_aaType_change <- aaVLFs.to.modalchanges(aminoAcid_Modal, birds_aaVLFreduced, 216)
## End(Not run)

VLF documentation built on Aug. 18, 2022, 5:06 p.m.