#' 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)
# }
# }
}
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