Frequency Matrix Approach for Assessing Very Low Frequency
Variants in Sequence Records
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Documentation for package ‘VLF’ version 1.1
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 |