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 |