Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

Description

Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures.

Details

vlfFun() aminoAcidFun() concordanceFun()

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Maintainer: Taryn B. T. Athey <tathey@uoguelph.ca>

Examples

## Not run: #VLF analysis
data(birds)
bird_vlfAnalysis <- vlfFun(birds)

#Amino Acid analysis
data(birds_aminoAcids)
bird_aaAnalysis <- aminoAcidFun(birds_aminoAcids)

#Concordance analysis
nuc_matrix <- bird_vlfAnalysis$VLFmatrix
aa_matrix <- bird_aaAnalysis$VLFmatrix
aa_modal <- bird_aaAnalysis$modal
bird_Concordance <- concordanceFun(nuc_matrix, aa_matrix, 648, 216, aa_modal)
## End(Not run)

VLF Decile Plot

Description

Creates a plot of VLF distributions summed for each decile segment.

Usage

Decile.Plot(VLF, seqlength)

Arguments

Value

A barplot containing the sum of the VLFs for each decile barcode segment.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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_position_VLFcount <- VLF.count.pos(birdSpec.freq, 0.001, 648)
Decile.Plot(Bird_position_VLFcount, 648)
## End(Not run)

Error Rate

Description

Calculates shared, singleton, and total second codon position error rate in a matrix of sequences.

Usage

Error.Rate(single, shared, spec, seqlength)

Arguments

Details

The arguments single and shared can be calculated simultaneously using the find.singles function. The spec argument can be calculated by using the nrow() function on the sequence matrix.

Value

A vector containing the single, shared, and total error rate based on the number of second position VLFs.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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_position_VLFcount <- VLF.count.pos(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)
Bird_error <- Error.Rate(birds_singleAndShared[1,], birds_singleAndShared[2,], specimen.Number, 648)
## End(Not run)

Modal Sequence

Description

Calculates the nucleotide sequence that occurs most often in a matrix of sequences.

Usage

MODE(freq, seqlength)

Arguments

Details

The argument freq can be calculated using the function ffrequency.matrix.function.

Value

A vector containing the first modal sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
## End(Not run)

Modal Frequencies

Description

Returns the frequencies of the nucleotides in each position of nucleotide sequence that occurs most often.

Usage

MODE.freq(freq, seqlength)

Arguments

Details

The argument freq can be calculated using the function ffrequency.matrix.function.

Value

A vector of frequencies for the first modal sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
Bird_first.modal.frequencies <- MODE.freq(frequency.matrix, 648)
## End(Not run)

Second Modal Frequency

Description

Calculates the frequencies of the nucleotides that occur second most often in a matrix of sequences.

Usage

MODE.second.freq(freq, seqlength)

Arguments

Details

The argument freq can be calculated using the function ffrequency.matrix.function.

Value

A vector containing the frequencies of the nucleotide sequence that occurs second most often.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
Bird_first.modal.frequencies <- MODE.freq(frequency.matrix, 648)
Bird_second.modal.frequencies <- MODE.second.freq(frequency.matrix, 648)
## End(Not run)

Sliding Window

Description

Creates a sliding window analysis plot for the VLFs in a matrix of sequences.

Usage

Sliding.Window(VLF, seqlength, n = 30)

Arguments

Details

The argument VLF can be calculated using the function VLF.count.pos for all VLFs, or find.singles for singleton and shared VLFs.

Value

A sliding window plot for the VLFs in each position of the barcode averaged over n.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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_position_VLFcount <- VLF.count.pos(birdSpec.freq, 0.001, 648)
Sliding.Window(Bird_position_VLFcount, 648)
## End(Not run)

Amino Acid VLFs

Description

Converts a matrix of amino acid frequencies into a matrix of amino acids.

Usage

VLF.aminoAcids(convert.matrix, seq.matrix, seqlength)

Arguments

Details

The argument convert.matrix can be calculated using the function aa.VLF.convert.matrix

Value

A matrix containing only aaVLFs and NAs in every other position of the sequence.

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)
## End(Not run)

VLF Matrix Convert

Description

Converts a matrix of nucleotide frequencies for each specimen into a matrix consisting entirely of very low frequency variant (VLF) frequencies and NAs in each other position.

Usage

VLF.convert.matrix(seq.matrix, freq, p, seqlength)

Arguments

Details

The argument freq can be calculated using the function specimen.frequencies.

Value

A matrix of VLF nucleotide frequencies, containing only those nucleotide frequencies that occur less than the designation p value, and NAs in each other position of the matrix.

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)
## End(Not run)

VLF Count for Sequence Positions

Description

Calculates the number of very low frequency variants (VLFs) in each position in a matrix of sequences.

Usage

VLF.count.pos(freq, p, seqlength)

Arguments

Details

The argument freq can be calculated using the specimen.frequencies function.

Value

A vector containing the number of VLFs for each position in the sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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_position_VLFcount <- VLF.count.pos(birdSpec.freq, 0.001, 648)
## End(Not run)

VLF Count for Specimens

Description

Calculates the number of very low frequency variants (VLFs) for each specimen in a matrix of sequence nucleotide frequencies.

Usage

VLF.count.spec(freq, p, seqlength)

Arguments

Details

The argument freq can be calculated using the function specimen.frequencies.

Value

A vector containing the number of VLFs for each specimen in the matrix.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
## End(Not run)

Nucleotide VLF Convert

Description

Converts a matrix of nucleotide frequencies for each specimen into a matrix of nucleotides for each specimen.

Usage

VLF.nucleotides(convert.matrix, seq.matrix, seqlength)

Arguments

Details

The argument convert.matrix can be calculated using the function VLF.convert.matrix.

Value

A matrix containing only ntVLFs in each position of the sequences, and NAs in all other positions.

Examples

## Not run: 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)
## End(Not run)

Reduced VLF Matrix

Description

Reduces a matrix of very low frequency variants (VLFs) so that only those specimen that contain VLFs remain in the matrix.

Usage

VLF.reduced(NA.matrix, sCount, seqlength)

Arguments

Details

The argument NA.matrix can be calculated using the function VLF.convert.matrix and VLF.nucleotides. The argument sCount can be calculated using the function VLF.count.spec.

Value

A matrix containing only those specimen that have VLFs, and only VLFs in their positions in the sequence, all other positions contain NAs.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
## End(Not run)

Amino Acid Modal Sequence

Description

Calculates the amino acid sequence that occurs most often in a matrix of amino acid sequences

Usage

aa.MODE(freq.matrix, seqlength)

Arguments

Details

The argument freq.matrix can be calculated using the function aa.frequency.matrix.function

Value

A vector containing the amino acid sequence that occurs most often.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
aminoAcid_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
## End(Not run)

Amino Acid Modal Frequencies

Description

Returns the frequencies of the amino acids that occur most often in each position of the sequence.

Usage

aa.MODE.freq(freq.matrix, seqlength)

Arguments

Details

The argument freq.matrix can be calculated using the function aa.frequency.matrix.function

Value

A vector of frequencies for the first modal sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
aminoAcid_firstModalFreq <- aa.MODE.freq(aminoAcid_frequency.Matrix, 216)
## End(Not run)

Amino Acid Second Modal Frequency

Description

Returns the frequencies of the amino acids that occur second most often in each position of a matrix of amino acid sequences.

Usage

aa.MODE.second.freq(freq.matrix, seqlength)

Arguments

Details

The argument freq.matrix can be calculated using the function aa.frequency.matrix.function

Value

A vector containing the frequencies of the second modal amino acid sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
aminoAcid_secondModalFreq <- aa.MODE.second.freq(aminoAcid_frequency.Matrix, 216)
## End(Not run)

Convert Amino Acid Matrix

Description

Converts a matrix of amino acid frequencies for each specimen into a matrix consisting of only VLF values and NAs in every non-VLF position.

Usage

aa.VLF.convert.matrix(seq.matrix, freq, p, seqlength)

Arguments

Value

A matrix of VLF amino acid frequencies, containing only those nucleotide frequencies that occur less than the designation p value, and NAs in each other position of the matrix.

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)
birds_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aminoAcid_frequencies, 0.001, 
    216)
## End(Not run)

VLF position count

Description

Calculates the number of very low frequency variants in each position in a matrix of sequences

Usage

aa.VLF.count.pos(freq, p, seqlength)

Arguments

Value

A vector containing the amino acid VLF count for each position of the sequence.

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)
birds_aminoAcid_positionVLFcount <- aa.VLF.count.pos(bird_aminoAcid_frequencies, 0.001, 216)
## End(Not run)

VLF Specimen Count

Description

Calculates the number of very low frequency variants for each specimen in a matrix of sequences.

Usage

aa.VLF.count.spec(freq, p, seqlength)

Arguments

Value

A vector containing the aaVLF count for every specimen.

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)
birds_aminoAcid_specimenVLFcount <- aa.VLF.count.spec(bird_aminoAcid_frequencies, 0.001, 216)
## End(Not run)

Amino Acid Reduced

Description

Reduces a matrix of amino acid very low frequency variants (aaVLFs) so that only those specimen that contain aaVLFs remain

Usage

aa.VLF.reduced(NA.matrix, sCount, seqlength)

Arguments

Details

The argument NA.matrix can be calculated using aa.VLF.convert.matrix and VLF.aminoAcids, the sCount argument can be calculaed using the aa.VLF.count.spec function.

Value

A matrix containing only specimen with aaVLFs, and only the aaVLF values in the sequences. All other positions of the sequence contain NAs.

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)
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)
## End(Not run)

Amino Acid Comparison

Description

Compares amino acid very low frequency variants between specimen of the same species

Usage

aa.compare(x, seqlength)

Arguments

Details

The argument x can be calculated using the separate function.

Value

A matrix containing two vectors, one with singleton VLF counts for each position of the sequence, and one with shared VLF counts for each position of the sequence.

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)
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)
## End(Not run)

First Modal Amino Acid Conservation

Description

Calculates the conservation of the first amino acids that occur most often in a matrix of amino acid sequences.

Usage

aa.conservation_first(modal, p, seqlength)

Arguments

Details

The item modal can be calculated using the aa.MODE.freq function.

Value

A vector that contains how many amino acids from the first modal sequence are conserved at the specified conservation level.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
aminoAcid_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
aminoAcid_firstModalFreq <- aa.MODE.freq(aminoAcid_frequency.Matrix, 216)
aminoAcid_firstConservation_100 <- aa.conservation_first(aminoAcid_firstModalFreq, 1, 216)
## End(Not run)

First and Second Modal Amino Acid Conservation

Description

Calculates the conservation of the amino acids that occur first and second most often in a matrix of sequences

Usage

aa.conservation_two(modal1, modal2, p, seqlength)

Arguments

Details

The argument modal1 can be calculated using the aa.MODE.freq function, and the argument modal2 can be calculated using he aa.MODE.second.freq function.

Value

A vector that contains how many amino acids from the first and second modal sequences are conserved at the specified conservation level.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
aminoAcid_Modal <- aa.MODE(aminoAcid_frequency.Matrix, 216)
aminoAcid_firstModalFreq <- aa.MODE.freq(aminoAcid_frequency.Matrix, 216)
aminoAcid_secondModalFreq <- aa.MODE.second.freq(aminoAcid_frequency.Matrix, 216)
aminoAcid_secondConservation_99.9 <- aa.conservation_two(aminoAcid_firstModalFreq, 
    aminoAcid_secondModalFreq, 0.999, 216)
## End(Not run)

Amino Acid Count

Description

Counts the number of each amino acid in each positino of the barcode.

Usage

aa.count.function(aminoAcids, seqlength)

Arguments

Details

The first and second column of the aminoAcid argument must contain the unique specimen identifier and the species name, respectively, followed by the amino acid sequence.

Value

A matrix containing the number of each amino acid in each position of the sequence. Each row is a different amino acid count, while the columns represent the sequence position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
## End(Not run)

Find amino acid singles

Description

Determines the number of shared and singleton amino acid VLFs.

Usage

aa.find.singles(aaSpecies, seqlength)

Arguments

Details

The argument aaSpecies contains only amino acid VLFs, and NAs in any other position in the sequence. The list can be created using the separate function.

Value

A matrix containing the number of singleton and shared aaVLFs in each position of the barcode.

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)
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)
## End(Not run)

Amino Acid Frequency Matrix

Description

Calculates the frequency of each amino acid.

Usage

aa.frequency.matrix.function(aa.count, seqlength)

Arguments

Details

The aa.count argument can be calculated using the function aa.count.function

Value

A matrix of the frequencies for each amino acid in each position of the barcode sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aminoAcid_frequency.Matrix <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
## End(Not run)

Specimen Nucleotide Frequencies

Description

Converts a matrix of amino acid sequences into a matrix of amino acid frequencies.

Usage

aa.specimen.frequencies(freq, seq.matrix, spec.names, seqlength)

Arguments

Details

The argument freq can be calculated using the function aa.frequency.matrix.function.

Value

A matrix containing the frequencies of each amino acid in the sequence.

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)
## End(Not run)

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

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)

Matching Amino Acid Positions

Description

Gives the position and residue of the amino acid VLFs in a matrix containing amino acid VLFs and NAs.

Usage

aminoAcid.matching.positions(matchAA, aalength)

Arguments

Details

The argument matchAA can be calculated usingthe find.matching function and taking the first argument from the returned value.

Value

A list for each aaVLF with a matching specimen identifier to a ntVLF. The first position in each entry of the list contains the specimen identifier, the second position contains the species name, the third position contains the sequence position of the aaVLF, and the fourth position contains the aaVLF.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## 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)
position_matchingNuc <- nucleotide.matching.positions(VLF_match[[2]], 648)
position_matchingAA <- aminoAcid.matching.positions(VLF_match[[1]], 216)
## End(Not run)

Amino Acid VLF Analysis Function

Description

Runs the full amino acid VLF analysis for the user and outputs results.

Usage

aminoAcidFun(x, p = 0.001, seqlength = 216, own = NULL)

Arguments

Value

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds_aminoAcids)
bird_aaAnalysis <- aminoAcidFun(birds_aminoAcids)
## End(Not run)

Bird Nucleotide Sequences

Description

Data set containing nucleotide sequences for 11,333 bird barcodes.

Usage

data(birds)

Format

The format is: chr [1:11333, 1:650] "gi|359280039|gb|JQ173884.1|" ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:650] "V1" "V2" "V3" "V4" ...

Source

Stoeckle, M. Y. and Kerr, K. C. R. (2012) Frequency Matrix Approach Demonstrates High Sequence Quality in Avian BARCODEs and Highlights Cryptic Pseudogenes. PLoS ONE. 7, e43992.

Examples

## Not run: data(birds)

Bird Amino Acid Sequences

Description

Data set containing amino acid sequences for 11,333 bird barcodes.

Usage

data(birds_aminoAcids)

Format

The format is: chr [1:11333, 1:218] "gi|359280039|gb|JQ173884.1|" ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:218] "V1" "V2" "V3" "V4" ...

Source

Stoeckle, M. Y. and Kerr, K. C. R. (2012) Frequency Matrix Approach Demonstrates High Sequence Quality in Avian BARCODEs and Highlights Cryptic Pseudogenes. PLoS ONE. 7, e43992.

Examples

## Not run: data(birds_aminoAcids)

Compare VLFs within Species

Description

Compares VLFs between specimen of the same species.

Usage

compare(x, seqlength)

Arguments

Details

List of sequences by species names, x, can be created using the separate function

Value

A matrix containing two vectors, one with singleton VLF counts for each position of the sequence, and one with shared VLF counts for each position of the sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)

#The compare function is called on from within the find.singles function
birds_singleAndShared <- find.singles(bird_species, 648)
## End(Not run)

VLF Concordance Check Function

Description

Compares ntVLFs to aaVLFs to see if they are concordant (i.e., if the ntVLF causes the aaVLF).

Usage

concordanceFun(nuc, aa, nuclength = 648, aalength = 216, aminoAcid_Modal)

Arguments

Details

The argument nuc can be taken from the VLFmatrix output from the vlfFun function. The argument aa can be taken from the VLFmatrix output from the aminoAcidFun function. The argument aminoAcid_Modal can be taken from the modal output from the aminoAcidFun function.

Value

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: #VLF analysis
data(birds)
bird_vlfAnalysis <- vlfFun(birds)

#Amino Acid analysis
data(birds_aminoAcids)
bird_aaAnalysis <- aminoAcidFun(birds_aminoAcids)

#Concordance analysis
bird_Concordance <- concordanceFun(bird_vlfAnalysis$VLFmatrix, bird_aaAnalysis$VLFmatrix, 648, 216,
    bird_aaAnalysis$modal)
## End(Not run)

Concordant Residue Changes

Description

Deternubes how many concordant aaVLFs have changed type of amino acid from the modal amino acid sequence. Amino acid residue types are polar charged, polar uncharged, non-polar, and amino acids with a unique side group.

Usage

concordant.to.modalchanges(matched, modal)

Arguments

Details

The matched argument can be calculated using the overall.matched function. The modal argument can be calculated using the aa.MODE function.

Value

A vector containing the number of concordant aaVLFs that changed amino acid residue type, and the number that contained the same residue type.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## 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)
position_matchingNuc <- nucleotide.matching.positions(VLF_match[[2]], 648)
position_matchingAA <- aminoAcid.matching.positions(VLF_match[[1]], 216)
matching_comparison <- overall.matched(position_matchingNuc, position_matchingAA, 648, 216)
concordant_aaType_change <- concordant.to.modalchanges(matching_comparison, aminoAcid_Modal)
## End(Not run)

First Modal Conserved

Description

Calculates the conservation of the nucleotides that occur most often in a matrix of sequences/

Usage

conservation_first(modal, p, seqlength)

Arguments

Details

The argument modal can be calculated using the MODE.freq function.

Value

A vector that contains how many nucleotides from the first modal sequence are conserved at the specified conservation level for each codon position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
Bird_first.modal.frequencies <- MODE.freq(frequency.matrix, 648)
First_conserved_100 <- conservation_first(Bird_first.modal.frequencies, 1, 648)
First_conserved_99.9 <- conservation_first(Bird_first.modal.frequencies, 0.999, 648)
## End(Not run)

First and Second Modal Conserved

Description

Calculates the conservation of the nucleotides that occur first and second most often in a matrix of sequences.

Usage

conservation_two(modal1, modal2, p, seqlength)

Arguments

Details

The argument modal1 can be calculated using the function MODE.freq. The argument modal2 can be calculated using the function MODE.second.freq.

Value

A vector that contains how many nucleotides from the first and second modal sequences are conserved at the specified conservation level for each codon position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
nucleotide.modalSequence <- MODE(frequency.matrix, 648)
Bird_first.modal.frequencies <- MODE.freq(frequency.matrix, 648)
Bird_second.modal.frequencies <- MODE.second.freq(frequency.matrix, 648)
FirstAndSecond_conserved_99.9 <- conservation_two(Bird_first.modal.frequencies, 
    Bird_second.modal.frequencies, 0.999, 648)
## End(Not run)

Nucleotide Count

Description

Counts the number of each dNTP in each position of an aligned barcode matrix.

Usage

count.function(nucleotides, spec.no, seqlength)

Arguments

Value

A matrix containing the number of each nucleotide in each position of the sequence. Each row is a different dNTP count, while the columns represent the sequence position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds)
Nuc.count <- count.function(birds, specimen.Number, 648)
## End(Not run)

Read Fasta Files

Description

Reads in fasta files and converts into sequence matrix

Usage

fasta.read(file, seqlength = 648, pos1 = 1, pos2 = 3)

Arguments

Value

A matrix of sequences, with the unique specimen identifers in the first column, the species names in the second column, and the sequence starting in the third column.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Frequency Matrix

Description

Calculates the frequency of each dNTP in each position of a nucleotide count matrix.

Usage

ffrequency.matrix.function(count.matrix, seqlength)

Arguments

Details

The argument count.matrix can be calculated using the function count.function.

Value

A matrix of the frequencies for each dNTP in each position of the barcode sequence.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: #Nucleotide VLF analysis
data(birds)
Nuc.count <- count.function(birds, specimen.Number, 648)
frequency.matrix <- ffrequency.matrix.function(Nuc.count, 648)
## End(Not run)

Find Matching ntVLF and aaVLF Specimen.

Description

Compares a list of aaVLF and ntVLF matrices for common specimen identifiers.

Usage

find.matching(NucleotideList, AminoAcidList, nuclength, aalength)

Arguments

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.

Value

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

## 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)

Single and Shared VLF Find

Description

Calculates the number of singleton and shared VLFs for each position of the nucleotide, by first seeing if there is only one specimen for a species, and then calling on the compare() function to calculate the number of singleton and shared VLFs for those species with multiple specimen.

Usage

find.singles(species, seqlength)

Arguments

Details

The argument species can be calculated using the separate function.

Value

A matrix containing the number of singleton and shared ntVLFs in each position of the barcode.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## 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)
## End(Not run)

Codon Position of Matching aa and ntVLFs

Description

Counts which codon positions of ntVLFs lead to the concordant aaVLF.

Usage

matched.codon.position(matched)

Arguments

Details

The argument matched can be calculated using the function overall.matched.

Value

A vector containing the number of concordant VLFs caused by ntVLFs in each codon position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## 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)
position_matchingNuc <- nucleotide.matching.positions(VLF_match[[2]], 648)
position_matchingAA <- aminoAcid.matching.positions(VLF_match[[1]], 216)
matching_comparison <- overall.matched(position_matchingNuc, position_matchingAA, 648, 216)
matching_codons <- matched.codon.position(matching_comparison)
## End(Not run)

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)

Arguments

Details

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

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.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## 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)
position_matchingNuc <- nucleotide.matching.positions(VLF_match[[2]], 648)
## End(Not run)

Final Matching

Description

Compares the ntVLFs and aaVLFs with the same specimen identifier, and determines which ntVLFs are concordant with aaVLFs.

Usage

overall.matched(positionNuc, positionAA, nuclength, aalength)

Arguments

Details

The argument positionNuc can be calculated using the function nucleotide.matching.positions. The argument positionAA can be calculated using the function aminoAcid.matching.positions.

Value

A list of 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, the aaVLF in the third position of each entry, the amino acid position of the aaVLF in the fourth entry, and the codon position of the concordant ntVLF in each position of the entry. If multiple ntVLFs have concordance with one aaVLF, then that aaVLF may contain multiple entries in the list, one for each ntVLF.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## 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_aa_speciesNames <- birds_aminoAcids[,2]
aminoAcids_specimenNumber <- nrow(birds_aminoAcids)
birds_aminoAcid_count <- aa.count.function(birds_aminoAcids, 216)
aa_freq.Mat <- aa.frequency.matrix.function(birds_aminoAcid_count, 216)
bird_aa_freq <- aa.specimen.frequencies(aa_freq.Mat, birds_aminoAcids, birds_aa_speciesNames, 216)
aminoAcid_Modal <- aa.MODE(aa_freq.Mat, 216)
birds_aminoAcid_specimenVLFcount <- aa.VLF.count.spec(bird_aa_freq, 0.001, 216)
birds_aaVLFconvert <- aa.VLF.convert.matrix(birds_aminoAcids, bird_aa_freq, 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)
position_matchingAA <- aminoAcid.matching.positions(VLF_match[[1]], 216)
matching_comparison <- overall.matched(position_matchingNuc, position_matchingAA, 648, 216)
## End(Not run)

Separate Specimen by Species Names

Description

Separates specimen into lists by species names.

Usage

separate(x)

Arguments

Details

If the argument x needs to be a reduced matrix, it can be calculated using the function VLF.reduced.

Value

A list containing a matrix of sequences for each species.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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_position_VLFcount <- VLF.count.pos(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)
## End(Not run)

Specimen Nucleotide Frequencies

Description

Converts a matrix of sequences into a matrix of nucleotide frequencies.

Usage

specimen.frequencies(freq, seq.matrix, no.spec, spec.names, seqlength)

Arguments

Details

The argument freq can be calculated using the function ffrequency.matrix.function. The number of specimen can be calculated by using the nrow() function on seq.matrix.

Value

A matrix containing the unique specimen identifer in the first position, the species name in the second position, and the frequencies for each nucleotide in the sequences starting at the third position.

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: 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)
## End(Not run)

Nucleotide VLF Assessment Function

Description

Runs the full nucleotide VLF analysis for the user and outputs the results.

Usage

vlfFun(x, p = 0.001, seqlength = 648, own = NULL)

Arguments

Value

Author(s)

Taryn B. T. Athey and Paul D. McNicholas

Examples

## Not run: data(birds)
bird_vlfAnalysis <- vlfFun(birds)
## End(Not run)