Other packages > Find by keyword >

VLF  

Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
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", "1.1-3")



Attach the package and use:
library("VLF")
Maintained by
Taryn B. T. Athey
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2013-11-19
Latest Update: 2025-04-10
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 1.1-3, https://cran.r-project.org/web/packages/VLF. Accessed 07 Mar. 2026.
Previous versions and publish date:
1.0 (2013-11-19 16:55), 1.1 (2022-08-18 14:30)
Other packages that cited VLF R package
View VLF citation profile
Other R packages that VLF depends, imports, suggests or enhances
Complete documentation for VLF
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
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

testDriveR  
Teaching Data for Statistics and Data Science
Provides data sets for teaching statistics and data science courses. It includes a sample of data f ...
Download / Learn more Package Citations See dependency  
portalr  
Create Useful Summaries of the Portal Data
Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Projec ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
ReviewR  
A Light-Weight, Portable Tool for Reviewing Individual Patient Records
A portable Shiny tool to explore patient-level electronic health record data and perform chart revi ...
Download / Learn more Package Citations See dependency  
lmSubsets  
Exact Variable-Subset Selection in Linear Regression
Exact and approximation algorithms for variable-subset selection in ordinary linear regression mode ...
Download / Learn more Package Citations See dependency  
SAMtool  
Stock Assessment Methods Toolkit
Simulation tools for closed-loop simulation are provided for the 'MSEtool' operating model to inform ...
Download / Learn more Package Citations See dependency  

26,264

R Packages

223,360

Dependencies

70,376

Author Associations

26,265

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA