R/gl2sa.r

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

#' @name gl2sa 
#' @title Converts genlight objects to the format used in the SNPassoc package
#' @family linker

#' @description
#' 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 installed Switch to run the function once SNPassoc package i
#' s installed [default FALSE].#' @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 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].

#' @author Bernd Guber (Post to \url{https://groups.google.com/d/forum/dartr})
#' 
#' @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.
#' @importFrom SNPassoc setupSNP
#' @export
#' @return Returns an object of class 'snp' to be used with SNPassoc.

gl2sa <- function(x,
                  installed = FALSE,
                  verbose = NULL
                  ) {
    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",
                             verbose = 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)
        }
    }
}