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VLF.R

](https://travis-ci.com/jphill01/VLF.R)

An R implementation of Stoeckle and Kerr's (2012) frequency matrix approach to assess very low frequency variants in DNA sequences (DOI: 10.1371/journal.pone.0043992).

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Version

Install

install.packages('VLF')

Monthly Downloads

401

Version

1.1-3

License

GPL (>= 3)

Maintainer

Taryn T. Athey

Last Published

April 10th, 2025

Functions in VLF (1.1-3)

aa.MODE

Amino Acid Modal Sequence
aa.MODE.freq

Amino Acid Modal Frequencies
aa.MODE.second.freq

Amino Acid Second Modal Frequency
aa.VLF.count.pos

VLF position count
aa.compare

Amino Acid Comparison
aa.VLF.count.spec

VLF Specimen Count
aminoAcid.matching.positions

Matching Amino Acid Positions
compare

Compare VLFs within Species
aminoAcidFun

Amino Acid VLF Analysis Function
ffrequency.matrix.function

Frequency Matrix
fasta.read

Read Fasta Files
concordanceFun

VLF Concordance Check Function
aa.count.function

Amino Acid Count
aa.conservation_two

First and Second Modal Amino Acid Conservation
birds

Bird Nucleotide Sequences
aa.find.singles

Find amino acid singles
aa.frequency.matrix.function

Amino Acid Frequency Matrix
matched.codon.position

Codon Position of Matching aa and ntVLFs
overall.matched

Final Matching
separate

Separate Specimen by Species Names
specimen.frequencies

Specimen Nucleotide Frequencies
birds_aminoAcids

Bird Amino Acid Sequences
aa.VLF.reduced

Amino Acid Reduced
aa.specimen.frequencies

Specimen Nucleotide Frequencies
aaVLFs.to.modalchanges

Amino Acid Changes
nucleotide.matching.positions

Matching Nucleotide Positions
conservation_two

First and Second Modal Conserved
find.matching

Find Matching ntVLF and aaVLF Specimen.
aa.conservation_first

First Modal Amino Acid Conservation
count.function

Nucleotide Count
find.singles

Single and Shared VLF Find
concordant.to.modalchanges

Concordant Residue Changes
conservation_first

First Modal Conserved
vlfFun

Nucleotide VLF Assessment Function
Error.Rate

Error Rate
MODE.freq

Modal Frequencies
VLF.convert.matrix

VLF Matrix Convert
MODE.second.freq

Second Modal Frequency
MODE

Modal Sequence
VLF-package

Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
Decile.Plot

VLF Decile Plot
Sliding.Window

Sliding Window
VLF.aminoAcids

Amino Acid VLFs
VLF.count.pos

VLF Count for Sequence Positions
VLF.count.spec

VLF Count for Specimens
VLF.nucleotides

Nucleotide VLF Convert
aa.VLF.convert.matrix

Convert Amino Acid Matrix
VLF.reduced

Reduced VLF Matrix