find.matching: Find Matching ntVLF and aaVLF Specimen.

In VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

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

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.

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)

VLF documentation built on Aug. 18, 2022, 5:06 p.m.