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.
Version: 1.15.0 Depends: R (≥ 3.0.1) Imports: ape, dplyr, graphics, grDevices, magrittr, memuse, methods, pinfsc50, Rcpp, stats, stringr, tibble, utils, vegan, viridisLite LinkingTo: Rcpp Suggests: adegenet, ggplot2, knitr, poppr, reshape2, rmarkdown, scales, testthat, tidyr Published: 2023-12-08 DOI: 10.32614/CRAN.package.vcfR Author: Brian J. Knaus [cre, aut], Niklaus J. Grunwald [aut], Eric C. Anderson [ctb], David J. Winter [ctb], Zhian N. Kamvar [ctb], Javier F. Tabima [ctb] Maintainer: Brian J. Knaus <briank.lists at gmail.com> License: GPL-3 URL: https://github.com/knausb/vcfR, https://knausb.github.io/vcfR_documentation/ NeedsCompilation: yes Citation: vcfR citation info Materials: README CRAN checks: vcfR results Documentation: Downloads: Reverse dependencies: Reverse imports: ApplyPolygenicScore, BIGr, CaMutQC, cardelino, castgen, diemr, epinetr, GARCOM, geneHapR, geneNR, GenomeAdmixR, MADSEQ, mappoly, MixviR, numbat, onemap, PopGenHelpR, Qploidy, RADstackshelpR, vivaldi, whoa Reverse suggests: coreCollection, dartR, dartR.base, MoBPS, pcadapt, rehh, sequoia, statgenGWAS Linking:Please use the canonical form https://CRAN.R-project.org/package=vcfR to link to this page.
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