VLF (version 1.1)

aaVLFs.to.modalchanges: 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)

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.

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.

Author

Taryn B. T. Athey and Paul D. McNicholas

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.

Examples

if (FALSE) 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)