# Find Matching ntVLF and aaVLF Specimen. Compares a list of aaVLF and ntVLF matrices for common specimen identifiers. ```r find.matching(NucleotideList, AminoAcidList, nuclength, aalength) ``` ## Arguments - `NucleotideList`: Matrix of VLF nucleotide sequences containing the only the nucleotidies that are VLFs and NAs in the other positions of the sequences. - `AminoAcidList`: Matrix of VLF amino acid sequences containing only the aaVLFs and NAs in the other positions of the sequences. - `nuclength`: Length of the nucleotide sequence (should be 3X the length of the amino acid sequence). - `aalength`: Length of the amino acid sequence (should be 1/3 the length of the nucleotide sequence). ## Details The argument NucleotideList can be calculated using the VLF.convert.matrix, VLF.nucleotides, and VLF.reduced functions. The argument AminoAcidList can be calculated using the aa.VLF.convert.matrix, VLF.aminoAcids, and aa.VLF.reduced functions. ## Returns A list containing matrices of aaVLFs in the first position and ntVLFs in the second position who have matching specimen identifiers. ## Author(s) Taryn B. T. Athey and Paul D. McNicholas ## Examples ```r ## Not run: #Nucleotide VLF analysis data(birds) species.names <- birds[,2] specimen.Number <- nrow(birds) rownames(birds) <- species.names Nuc.count <- count.function(birds, specimen.Number, 648) frequency.matrix <- ffrequency.matrix.function(Nuc.count, 648) birdSpec.freq <- specimen.frequencies(frequency.matrix, birds, specimen.Number, species.names, 648) Bird_specimen_VLFcount <- VLF.count.spec(birdSpec.freq, 0.001, 648) bird_VLFconvert <- VLF.convert.matrix(birds, birdSpec.freq, 0.001, 648) bird_VLFnuc <- VLF.nucleotides(bird_VLFconvert, birds, 648) bird_VLFreduced <- VLF.reduced(bird_VLFnuc, Bird_specimen_VLFcount, 648) bird_species <- separate(bird_VLFreduced) birds_singleAndShared <- find.singles(bird_species, 648) #Amino Acid VLF Analysis 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) birds_aaSpecies <- separate(birds_aaVLFreduced) birds_aminoAcid_singleAndShared <- aa.find.singles(birds_aaSpecies, 216) #Concordance Analysis VLF_match <- find.matching(bird_VLFreduced, birds_aaVLFreduced, 648, 216) ## End(Not run) ```

find.matching function