concordant.to.modalchanges: Concordant Residue Changes

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

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

matched	A list containing the concordant aaVLFs and their properties (e.g., sequence position).
modal	A vector containing the modal amino acid sequence.

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)

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