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

# Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records

## Documentation for package ‘VLF’ version 1.1-3

- DESCRIPTION file
- Package README

## Help Pages

VLF-package | Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
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
aminoAcid.matching.positions | Matching Amino Acid Positions
aminoAcidFun | Amino Acid VLF Analysis Function
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 | Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
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
VLF.nucleotides | Nucleotide VLF Convert
VLF.reduced | Reduced VLF Matrix
vlfFun | Nucleotide VLF Assessment Function