R/vcfR.R

In vcfR: Manipulate and Visualize VCF Data

# vcf.R.

#' Variant call format files processed with vcfR.
#'
#' vcfR provides a suite of tools for input and output of variant call format (VCF) files, manipulation of their content and visualization.
#' 
#' @details
#' 
#' 
#' \strong{File input and output} is facilitated with the functions \code{read.vcfR} and \code{write.vcf}.
#' Input of vcf format data results in an S4 \code{\link{vcfR-class}} object.
# ' Objects of class vcfR can be manipulated with \code{\link{vcfR-method}} and \code{\link{extract.gt}}.
#' Objects of class vcfR can be manipulated with \link[vcfR:vcfR-method]{vcfR-method} and \code{extract.gt}.
#' Contents of the vcfR object can be visualized with the \code{\link{plot}} method.
#' More complex visualizations can be created using a series of functions.
#' See \code{vignette(topic="sequence_coverage")} for an example.
#' Once manipulations are complete the object may be written to a *.vcf.gz format file using \code{write.vcf} or exported to objects supported by other R packages with \code{vcfR2genind} or \code{vcfR2loci}.
#' 
#' 
#' More complex visualization can be accomplished by converting a vcfR object to a \code{\link{chromR-class}} object.
#' An example exists on the \code{create.chromR} man page.
#' 
#' 
#' 
#' A \strong{complete list of functions} can be displayed with: library(help = vcfR).
#'
#' \strong{Vignettes} (documentation) can be listed with: \code{browseVignettes('vcfR')}.
#' 
#' 
#' Several example \strong{datasets} are included in vcfR.
#' \strong{vcfR_test} comes from the VCF specification and provides a vcfR object with a diversity of examples in a small dataset.
#' \strong{vcfR_example} is a subset of the pinfsc50 dataset that includes VCF, GFF and FASTA data for moderate sized testing.
#' The \href{https://cran.r-project.org/package=pinfsc50}{pinfsc50} dataset is available as a separate package and includes VCF, GFF and FASTA data for testing and benchmarking.
#'
#' @seealso 
#' More documentation for vcfR can be found at the \href{https://knausb.github.io/vcfR_documentation/}{vcfR documentation} website.
#'
#' 
#' 
#' @import pinfsc50
#' @import ape
#' @docType package
#' @name vcfR-package
# ' @rdname vcfR
#' @useDynLib vcfR, .registration = TRUE
#' @importFrom Rcpp sourceCpp
#' @importFrom stats setNames
#' 
#' 
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