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

aa.compareAmino Acid Comparison
aa.conservation_firstFirst Modal Amino Acid Conservation
aa.conservation_twoFirst and Second Modal Amino Acid Conservation
aa.count.functionAmino Acid Count
aa.find.singlesFind amino acid singles
aa.frequency.matrix.functionAmino Acid Frequency Matrix
aa.MODEAmino Acid Modal Sequence
aa.MODE.freqAmino Acid Modal Frequencies
aa.MODE.second.freqAmino Acid Second Modal Frequency
aa.specimen.frequenciesSpecimen Nucleotide Frequencies
aa.VLF.convert.matrixConvert Amino Acid Matrix
aa.VLF.count.posVLF position count
aa.VLF.count.specVLF Specimen Count
aa.VLF.reducedAmino Acid Reduced Acid Changes
aminoAcidFunAmino Acid VLF Analysis Function
aminoAcid.matching.positionsMatching Amino Acid Positions
birdsBird Nucleotide Sequences
birds_aminoAcidsBird Amino Acid Sequences
compareCompare VLFs within Species
concordanceFunVLF Concordance Check Function Residue Changes
conservation_firstFirst Modal Conserved
conservation_twoFirst and Second Modal Conserved
count.functionNucleotide Count
Decile.PlotVLF Decile Plot
Error.RateError Rate
fasta.readRead Fasta Files
ffrequency.matrix.functionFrequency Matrix
find.matchingFind Matching ntVLF and aaVLF Specimen.
find.singlesSingle and Shared VLF Find
matched.codon.positionCodon Position of Matching aa and ntVLFs
MODEModal Sequence
MODE.freqModal Frequencies
MODE.second.freqSecond Modal Frequency
nucleotide.matching.positionsMatching Nucleotide Positions
overall.matchedFinal Matching
separateSeparate Specimen by Species Names
Sliding.WindowSliding Window
specimen.frequenciesSpecimen Nucleotide Frequencies
VLF.aminoAcidsAmino Acid VLFs
VLF.convert.matrixVLF Matrix Convert
VLF.count.posVLF Count for Sequence Positions
VLF.count.specVLF Count for Specimens
vlfFunNucleotide VLF Assessment Function
VLF.nucleotidesNucleotide VLF Convert
VLF-packageFrequency Matrix Approach for Assessing Very Low Frequency...
VLF.reducedReduced VLF Matrix
VLF documentation built on May 1, 2019, 10:20 p.m.