VLF (version 1.1)

nucleotide.matching.positions: Matching Nucleotide Positions

Description

Calculates the position of the VLFs in a matrix contain ntVLFs whose specimen identifiers match identifiers of a matrix containing aaVLFs.

Usage

nucleotide.matching.positions(matchNuc, nuclength)

Value

A list for each ntVLF containing the specimen identifier in the first position of each list entry, the species name in the second position of each list entry, and the position of the ntVLF in the third position of each list entry.

Arguments

matchNuc

A matrix containing only of the nucleotides that are VLFs and NAs in all other positions of the sequences.

nuclength

The length of the nucleotide sequence.

Author

Taryn B. T. Athey and Paul D. McNicholas

Details

The argument matchNuc can be calculated using the function find.matching.

Examples

if (FALSE) #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)
position_matchingNuc <- nucleotide.matching.positions(VLF_match[[2]], 648)