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.

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

View on CRAN

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

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

Files

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

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