aminoAcid.matching.positions: Matching Amino Acid Positions

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

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

matchAA	A matrix containing aaVLFs and NAs in all other positions of the sequences.
aalength	Amino acid sequence length.

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)

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