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VLF
View on CRAN: Click
here
Download and install VLF package within the R console
Install from CRAN:
install.packages("VLF")
Install from Github:
library("remotes")
install_github("cran/VLF")
Install by package version:
library("remotes")
install_version("VLF", "1.1")
Attach the package and use:
library("VLF")
Maintained by
Taryn B. T. Athey
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-11-19
Latest Update: 2022-08-18
Description:
Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences.The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs.The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another.Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992>.
How to cite:
Taryn B. T. Athey (2013). VLF: Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records. R package version 1.1, https://cran.r-project.org/web/packages/VLF
Previous versions and publish date:
1.0 (2013-11-19 16:55)
Other packages that cited VLF R package
View VLF citation profile
Other R packages that VLF depends,
imports, suggests or enhances
Functions, R codes and Examples using
the VLF R package
Some associated functions: Decile.Plot . Error.Rate . MODE.freq . MODE . MODE.second.freq . Sliding.Window . VLF-package . VLF.aminoAcids . VLF.convert.matrix . VLF.count.pos . VLF.count.spec . VLF.nucleotides . VLF.reduced . aa.MODE.freq . aa.MODE . aa.MODE.second.freq . aa.VLF.convert.matrix . aa.VLF.count.pos . aa.VLF.count.spec . aa.VLF.reduced . aa.compare . aa.conservation_first . aa.conservation_two . aa.count.function . aa.find.singles . aa.frequency.matrix.function . aa.specimen.frequencies . aaVLFs.to.modalchanges . aminoAcid.matching.positions . aminoAcidFun . birds . birds_aminoAcids . compare . concordanceFun . concordant.to.modalchanges . conservation_first . conservation_two . count.function . fasta.read . ffrequency.matrix.function . find.matching . find.singles . matched.codon.position . nucleotide.matching.positions . overall.matched . separate . specimen.frequencies . vlfFun .
Some associated R codes: Decile.Plot.R . Error.Rate.R . MODE.R . MODE.freq.R . MODE.second.freq.R . Sliding.Window.R . VLF.aminoAcids.R . VLF.convert.matrix.R . VLF.count.pos.R . VLF.count.spec.R . VLF.nucleotides.R . VLF.reduced.R . aa.MODE.R . aa.MODE.freq.R . aa.MODE.second.freq.R . aa.VLF.convert.matrix.R . aa.VLF.count.pos.R . aa.VLF.count.spec.R . aa.VLF.reduced.R . aa.compare.R . aa.conservation_first.R . aa.conservation_two.R . aa.count.function.R . aa.find.singles.R . aa.frequency.matrix.function.R . aa.specimen.frequencies.R . aaVLFs.to.modalchanges.R . aminoAcid.matching.positions.R . aminoAcidFun.R . compare.R . concordanceFun.R . concordant.to.modalchanges.R . conservation_first.R . conservation_two.R . count.function.R . fasta.read.R . ffrequency.matrix.function.R . find.matching.R . find.singles.R . matched.codon.position.R . nucleotide.matching.positions.R . overall.matched.R . separate.R . specimen.frequencies.R . vlfFun.R . Full VLF package functions and examples
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