Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Maintainer: Brian J. Knaus <briank.lists at gmail.com>

Author(s): Brian J. Knaus*, Niklaus J. Grunwald*, Eric C. Anderson*, David J. Winter*, Zhian N. Kamvar*

Install package and any missing dependencies by running this line in your R console:

install.packages("vcfR")

Depends R (>= 3.0.1)
Imports ape, dplyr, graphics, grDevices, magrittr, memuse, methods, pinfsc50, Rcpp, stats, stringr, tidyr, utils, vegan, viridisLite
Suggests adegenet, ggplot2, knitr, poppr, reshape2, rmarkdown, scales, testthat
Enhances
Linking to Rcpp
Reverse
depends
pcadapt
Reverse
imports
Reverse
suggests
Reverse
enhances
Reverse
linking to

Package vcfR
Materials
URL
Task Views
Version 1.4.0
Published 2017-01-07
License GPL
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks vcfR check results
Package source vcfR_1.4.0.tar.gz