1d:T7fd,# Amino Acid Changes 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. ```r 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. ## Returns 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 ```r ## 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

aaVLFs.to.modalchanges function