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

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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.

Author
Taryn B. T. Athey and Paul D. McNicholas
Date of publication
2013-11-19 16:55:25
Maintainer
Taryn B. T. Athey <tathey@uoguelph.ca>
License
GPL (>= 3)
Version
1.0

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

Files in this package

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