Package: VLF 1.1

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

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. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992>.

Authors:Taryn B. T. Athey [aut, cre], Paul D. McNicholas [aut, cre], Jarrett D. Phillips [ctb]

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VLF.pdf |VLF.html✨
VLF/json (API)

# Install 'VLF' in R:
install.packages('VLF', repos = c('https://tathey.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

45 exports 0.36 score 0 dependencies 1 dependents 48 scripts 273 downloads

Last updated 2 years agofrom:bcfb0e6232. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winNOTESep 16 2024
R-4.5-linuxNOTESep 16 2024
R-4.4-winNOTESep 16 2024
R-4.4-macNOTESep 16 2024
R-4.3-winOKSep 16 2024
R-4.3-macOKSep 16 2024

Exports:aa.compareaa.conservation_firstaa.conservation_twoaa.count.functionaa.find.singlesaa.frequency.matrix.functionaa.MODEaa.MODE.freqaa.MODE.second.freqaa.specimen.frequenciesaa.VLF.convert.matrixaa.VLF.count.posaa.VLF.count.specaa.VLF.reducedaaVLFs.to.modalchangesaminoAcid.matching.positionsaminoAcidFuncompareconcordanceFunconcordant.to.modalchangesconservation_firstconservation_twocount.functionDecile.PlotError.Ratefasta.readffrequency.matrix.functionfind.matchingfind.singlesmatched.codon.positionMODEMODE.freqMODE.second.freqnucleotide.matching.positionsoverall.matchedseparateSliding.Windowspecimen.frequenciesVLF.aminoAcidsVLF.convert.matrixVLF.count.posVLF.count.specVLF.nucleotidesVLF.reducedvlfFun

Dependencies:

Readme and manuals

Help Manual

Help pageTopics
Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence RecordsVLF-package VLF
Amino Acid Comparisonaa.compare
First Modal Amino Acid Conservationaa.conservation_first
First and Second Modal Amino Acid Conservationaa.conservation_two
Amino Acid Countaa.count.function
Find amino acid singlesaa.find.singles
Amino Acid Frequency Matrixaa.frequency.matrix.function
Amino Acid Modal Sequenceaa.MODE
Amino Acid Modal Frequenciesaa.MODE.freq
Amino Acid Second Modal Frequencyaa.MODE.second.freq
Specimen Nucleotide Frequenciesaa.specimen.frequencies
Convert Amino Acid Matrixaa.VLF.convert.matrix
VLF position countaa.VLF.count.pos
VLF Specimen Countaa.VLF.count.spec
Amino Acid Reducedaa.VLF.reduced
Amino Acid ChangesaaVLFs.to.modalchanges
Matching Amino Acid PositionsaminoAcid.matching.positions
Amino Acid VLF Analysis FunctionaminoAcidFun
Bird Nucleotide Sequencesbirds
Bird Amino Acid Sequencesbirds_aminoAcids
Compare VLFs within Speciescompare
VLF Concordance Check FunctionconcordanceFun
Concordant Residue Changesconcordant.to.modalchanges
First Modal Conservedconservation_first
First and Second Modal Conservedconservation_two
Nucleotide Countcount.function
VLF Decile PlotDecile.Plot
Error RateError.Rate
Read Fasta Filesfasta.read
Frequency Matrixffrequency.matrix.function
Find Matching ntVLF and aaVLF Specimen.find.matching
Single and Shared VLF Findfind.singles
Codon Position of Matching aa and ntVLFsmatched.codon.position
Modal SequenceMODE
Modal FrequenciesMODE.freq
Second Modal FrequencyMODE.second.freq
Matching Nucleotide Positionsnucleotide.matching.positions
Final Matchingoverall.matched
Separate Specimen by Species Namesseparate
Sliding WindowSliding.Window
Specimen Nucleotide Frequenciesspecimen.frequencies
Amino Acid VLFsVLF.aminoAcids
VLF Matrix ConvertVLF.convert.matrix
VLF Count for Sequence PositionsVLF.count.pos
VLF Count for SpecimensVLF.count.spec
Nucleotide VLF ConvertVLF.nucleotides
Reduced VLF MatrixVLF.reduced
Nucleotide VLF Assessment FunctionvlfFun