R/gl2sa.r

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#' Converts genlight objects to the format used in the SNPassoc package
#'
#' This function exports a genlight object into a SNPassoc object. See package
#' SNPassoc for details. This function needs package SNPassoc. At the time of
#' writing (August 2020) the package was no longer available from CRAN. To
#' install the package check their github repository.
#' \url{https://github.com/isglobal-brge/SNPassoc} and/or use
#' \code{install_github('isglobal-brge/SNPassoc')} to install the function and
#' uncomment the function code.
#'
#' @param x Name of the genlight object containing the SNP data [required].
#' @param verbose Verbosity: 0, silent or fatal errors; 1, begin and end; 2,
#' progress log; 3, progress and results summary; 5, full report
#' [default 2 or as specified using gl.set.verbosity].
#' @param installed Switch to run the function once SNPassoc package i
#' s installed [default FALSE].
#' @export
#' @return Returns an object of class 'snp' to be used with SNPassoc.
#' @references
#' Gonzalez, J.R., Armengol, L., Sol?, X., Guin?, E., Mercader, J.M., Estivill,
#' X. and Moreno, V. (2017). SNPassoc: an R package to perform whole genome
#' association studies. Bioinformatics 23:654-655.
#' @author Bernd Guber (Post to \url{https://groups.google.com/d/forum/dartr})

gl2sa <- function(x,
                  verbose = NULL,
                  installed = FALSE) {
    sa <- NULL
    #Delete those lines if you have installed SNPassoc
    if (!installed) {
        cat(
            report(
                "This function requires the package SNPassoc, which is no longer supported by CRAN. See details in the help pages of the function ?gl2sa."
            )
        )
    }
    
    # #Change 'if (FALSE) {' below to 'if (TRUE) {' to run the function.
    # if (installed) {
    #     # CHECK IF PACKAGES ARE INSTALLED
    #     if (!(requireNamespace("parallel", quietly = TRUE))) {
    #         stop(
    #             error(
    #                 "Package parallel needed for this function to work. Please install it."
    #             )
    #         )
    #     }
    #     
    #     if (!(requireNamespace("pegas", quietly = TRUE))) {
    #         stop(error(
    #             "Package pegas needed for this function to work. Please install it."
    #         ))
    #     }
    #     
    #     if (!(requireNamespace("SNPassoc", quietly = TRUE))) {
    #         stop(
    #             error(
    #                 "To use this function you need to install package: SNPassoc. Please refer to the help of the function for instructions (?gl2sa)."
    #             )
    #         )
    #     } else {
    #         # SET VERBOSITY
    #         verbose <- gl.check.verbosity(verbose)
    #         
    #         # FLAG SCRIPT START
    #         funname <- match.call()[[1]]
    #         utils.flag.start(func = funname,
    #                          build = "Jody",
    #                          verbosity = verbose)
    #         
    #         # CHECK DATATYPE
    #         datatype <- utils.check.datatype(x, verbose = verbose)
    #         
    #         # DO THE JOB
    #         
    #         if (verbose >= 2) {
    #             cat(report("  Writing data to SNPassoc object\n"))
    #         }
    #         pop <- gl2gi(x)
    #         xxx <- pegas::as.loci(pop)[,-1]
    #         sa <- SNPassoc::setupSNP(data.frame(xxx), 1:ncol(xxx), )
    #         
    #         # FLAG SCRIPT END
    #         
    #         if (verbose > 0) {
    #             cat(report("Completed:", funname, "\n"))
    #         }
    #         
    #         return(sa)
    #     }
    # }
}