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#' Convert a loci object into a genind object
#'
#' @description This function is exactly the same as \code{loci2genind}
#' from \pkg{pegas} package
#'
#' @param x An object of class \code{loci} to convert
#' @param ploidy An integer indicating the ploidy level
#' (by default, 'ploidy = 2')
#' @param na.alleles A character vector indicating the coding of the alleles
#' to be treated as missing data (by default, 'na.alleles = c("NA")')
#' @return An object of class \code{genind}
#' @export
#' @author P. Savary
#' @examples
#' data("data_ex_loci")
#' genind <- loci_to_genind(data_ex_loci, ploidy = 2, na.alleles = "NA")
loci_to_genind <- function(x,
ploidy = 2,
na.alleles = c("NA")){
# Check whether 'x' is a 'loci' object
if(!inherits(x, "loci")){
stop("Input 'x' must be a 'loci' object.")
}
# Reorder individuals if necessary
if(!all(x$population == x$population[order(x$population)])){
message("Individuals in 'x' were not ordered, they have
been ordered by populations and populations ordered in alphabetic
order for the convertion.")
x <- x[order(x$population), ]
}
# Convert 'x' into a 'genind' object
data_genind <- pegas::loci2genind(x,
ploidy,
na.alleles)
return(data_genind)
}
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