nucleotide.matching.positions: Matching Nucleotide Positions

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

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

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.

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)

VLF documentation built on April 12, 2025, 1:22 a.m.