VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
Version 1.0

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.

AuthorTaryn B. T. Athey and Paul D. McNicholas
Date of publication2013-11-19 16:55:25
MaintainerTaryn B. T. Athey <tathey@uoguelph.ca>
LicenseGPL (>= 3)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("VLF")

Getting started

Package overview

Popular man pages

aa.conservation_two: First and Second Modal Amino Acid Conservation
aa.frequency.matrix.function: Amino Acid Frequency Matrix
aa.MODE.second.freq: Amino Acid Second Modal Frequency
aminoAcid.matching.positions: Matching Amino Acid Positions
conservation_two: First and Second Modal Conserved
Error.Rate: Error Rate
find.matching: Find Matching ntVLF and aaVLF Specimen.
See all...

All man pages Function index File listing

Man pages

aa.compare: Amino Acid Comparison
aa.conservation_first: First Modal Amino Acid Conservation
aa.conservation_two: First and Second Modal Amino Acid Conservation
aa.count.function: Amino Acid Count
aa.find.singles: Find amino acid singles
aa.frequency.matrix.function: Amino Acid Frequency Matrix
aa.MODE: Amino Acid Modal Sequence
aa.MODE.freq: Amino Acid Modal Frequencies
aa.MODE.second.freq: Amino Acid Second Modal Frequency
aa.specimen.frequencies: Specimen Nucleotide Frequencies
aa.VLF.convert.matrix: Convert Amino Acid Matrix
aa.VLF.count.pos: VLF position count
aa.VLF.count.spec: VLF Specimen Count
aa.VLF.reduced: Amino Acid Reduced
aaVLFs.to.modalchanges: Amino Acid Changes
aminoAcidFun: Amino Acid VLF Analysis Function
aminoAcid.matching.positions: Matching Amino Acid Positions
birds: Bird Nucleotide Sequences
birds_aminoAcids: Bird Amino Acid Sequences
compare: Compare VLFs within Species
concordanceFun: VLF Concordance Check Function
concordant.to.modalchanges: Concordant Residue Changes
conservation_first: First Modal Conserved
conservation_two: First and Second Modal Conserved
count.function: Nucleotide Count
Decile.Plot: VLF Decile Plot
Error.Rate: Error Rate
fasta.read: Read Fasta Files
ffrequency.matrix.function: Frequency Matrix
find.matching: Find Matching ntVLF and aaVLF Specimen.
find.singles: Single and Shared VLF Find
matched.codon.position: Codon Position of Matching aa and ntVLFs
MODE: Modal Sequence
MODE.freq: Modal Frequencies
MODE.second.freq: Second Modal Frequency
nucleotide.matching.positions: Matching Nucleotide Positions
overall.matched: Final Matching
separate: Separate Specimen by Species Names
Sliding.Window: Sliding Window
specimen.frequencies: Specimen Nucleotide Frequencies
VLF.aminoAcids: Amino Acid VLFs
VLF.convert.matrix: VLF Matrix Convert
VLF.count.pos: VLF Count for Sequence Positions
VLF.count.spec: VLF Count for Specimens
vlfFun: Nucleotide VLF Assessment Function
VLF.nucleotides: Nucleotide VLF Convert
VLF-package: Frequency Matrix Approach for Assessing Very Low Frequency...
VLF.reduced: Reduced VLF Matrix

Functions

Decile.Plot Man page Source code
Error.Rate Man page Source code
MODE Man page Source code
MODE.freq Man page Source code
MODE.second.freq Man page Source code
Sliding.Window Man page Source code
VLF Man page
VLF-package Man page
VLF.aminoAcids Man page Source code
VLF.convert.matrix Man page Source code
VLF.count.pos Man page Source code
VLF.count.spec Man page Source code
VLF.nucleotides Man page Source code
VLF.reduced Man page Source code
aa.MODE Man page Source code
aa.MODE.freq Man page Source code
aa.MODE.second.freq Man page Source code
aa.VLF.convert.matrix Man page Source code
aa.VLF.count.pos Man page Source code
aa.VLF.count.spec Man page Source code
aa.VLF.reduced Man page Source code
aa.compare Man page Source code
aa.conservation_first Man page Source code
aa.conservation_two Man page Source code
aa.count.function Man page Source code
aa.find.singles Man page Source code
aa.frequency.matrix.function Man page Source code
aa.specimen.frequencies Man page Source code
aaVLFs.to.modalchanges Man page Source code
aminoAcid.matching.positions Man page Source code
aminoAcidFun Man page Source code
birds Man page
birds_aminoAcids Man page
compare Man page Source code
concordanceFun Man page Source code
concordant.to.modalchanges Man page Source code
conservation_first Man page Source code
conservation_two Man page Source code
count.function Man page Source code
fasta.read Man page Source code
ffrequency.matrix.function Man page Source code
find.matching Man page Source code
find.singles Man page Source code
matched.codon.position Man page Source code
nucleotide.matching.positions Man page Source code
overall.matched Man page Source code
separate Man page Source code
specimen.frequencies Man page Source code
vlfFun Man page Source code

Files

NAMESPACE
data
data/birds_aminoAcids.rda
data/birds.rda
R
R/aa.VLF.count.pos.R
R/Decile.Plot.R
R/aa.VLF.count.spec.R
R/VLF.count.pos.R
R/aa.find.singles.R
R/aa.MODE.freq.R
R/overall.matched.R
R/MODE.second.freq.R
R/VLF-internal.R
R/conservation_two.R
R/find.matching.R
R/VLF.convert.matrix.R
R/find.singles.R
R/concordanceFun.R
R/conservation_first.R
R/Sliding.Window.R
R/vlfFun.R
R/aa.count.function.R
R/aaVLFs.to.modalchanges.R
R/aa.VLF.reduced.R
R/VLF.reduced.R
R/aa.frequency.matrix.function.R
R/matched.codon.position.R
R/Error.Rate.R
R/aa.conservation_two.R
R/nucleotide.matching.positions.R
R/VLF.nucleotides.R
R/VLF.count.spec.R
R/fasta.read.R
R/count.function.R
R/aminoAcidFun.R
R/VLF.aminoAcids.R
R/aa.conservation_first.R
R/MODE.R
R/aminoAcid.matching.positions.R
R/aa.MODE.R
R/concordant.to.modalchanges.R
R/aa.MODE.second.freq.R
R/aa.VLF.convert.matrix.R
R/compare.R
R/ffrequency.matrix.function.R
R/MODE.freq.R
R/specimen.frequencies.R
R/aa.specimen.frequencies.R
R/separate.R
R/aa.compare.R
MD5
DESCRIPTION
man
man/matched.codon.position.Rd
man/aa.frequency.matrix.function.Rd
man/VLF.aminoAcids.Rd
man/find.singles.Rd
man/Error.Rate.Rd
man/aa.VLF.count.pos.Rd
man/aa.VLF.reduced.Rd
man/aa.MODE.second.freq.Rd
man/aa.specimen.frequencies.Rd
man/VLF.reduced.Rd
man/conservation_first.Rd
man/conservation_two.Rd
man/ffrequency.matrix.function.Rd
man/aa.conservation_two.Rd
man/aminoAcid.matching.positions.Rd
man/aa.VLF.count.spec.Rd
man/MODE.freq.Rd
man/separate.Rd
man/aa.conservation_first.Rd
man/aminoAcidFun.Rd
man/Sliding.Window.Rd
man/find.matching.Rd
man/birds.Rd
man/aaVLFs.to.modalchanges.Rd
man/MODE.second.freq.Rd
man/VLF.count.spec.Rd
man/specimen.frequencies.Rd
man/aa.count.function.Rd
man/Decile.Plot.Rd
man/compare.Rd
man/VLF-package.Rd
man/fasta.read.Rd
man/count.function.Rd
man/overall.matched.Rd
man/aa.VLF.convert.matrix.Rd
man/VLF.convert.matrix.Rd
man/aa.compare.Rd
man/aa.find.singles.Rd
man/nucleotide.matching.positions.Rd
man/aa.MODE.Rd
man/vlfFun.Rd
man/concordanceFun.Rd
man/VLF.nucleotides.Rd
man/concordant.to.modalchanges.Rd
man/VLF.count.pos.Rd
man/aa.MODE.freq.Rd
man/birds_aminoAcids.Rd
man/MODE.Rd
VLF documentation built on May 19, 2017, 11 a.m.

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