R/eco.convert.R

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

#' Conversion utility for genetic data
#' 
#' @description This function interconverts genetic data among matrix format 
#' (one locus or one allele per column) and list format 
#' (one locus or one allele per column).
#' @param X Input data.
#' @param input Input data format.
#' @param output Output data format.
#' @param ncod Number of digits coding each allele.
#' @param ploidy Ploidy of the data.
#' @param sep.in Character separating alleles in the input data if present.
#' @param sep.out Character separating alleles in the output data. Default 
#' option do not separate alleles.
#' @param chk.names Defalult TRUE. The function makes checks of individuals 
#' and loci names during conversion.
#' @param chk.plocod  Defalult TRUE. The function checks coherence 
#' in/between ploidy and number of digits coding alleles for loci data during conversion.
#' @examples
#' 
#' \dontrun{
#' 
#' data(eco3)
#' 
#' # One allele per column
#' loc2al <- eco.convert(eco3[["G"]], "matrix", "alleles.matrix", ploidy = 2)
#' loc2al     
#' 
#' # Inverse operation (collapse alleles into locus)
#' al2loc <- eco.convert(loc2al, "alleles.matrix", "matrix", ploidy = 2)
#' al2loc
#' 
#' # Separating alleles with a character string
#' loc2loc <- eco.convert(eco3[["G"]], "matrix", "matrix", ploidy = 2, sep.out = "/")
#' loc2loc
#' 
#' # Inverse operation (removing separator)
#' loc2loc.nosep <- eco.convert(loc2loc, "matrix", "matrix", ploidy = 2, sep.in = "/", sep.out = "")
#' loc2loc.nosep
#' 
#' # Locus to list
#' loc2list <- eco.convert(eco3[["G"]], "matrix", "list", ploidy = 2)
#' loc2list
#' 
#' # Locus to allele list
#' al2list <- eco.convert(eco3[["G"]], "matrix",  "alleles.list", ploidy = 2)
#' al2list
#' 
#' # The inverse operations are also defined. All the formats are interconvertible.
#' # Locus operations have defined a within operation (matrix to matrix, list to list), 
#' # with the purpose of put/remove separators between alleles. The program accepts any ploidy level. 
#' 
#' 
#' }
#' 
#' @author Leandro Roser \email{learoser@@gmail.com}
#' @export

setGeneric("eco.convert", function(X, 
                        input = c("matrix", "alleles.matrix", "list", "alleles.list"),
                        output = c("matrix", "alleles.matrix", "list", "alleles.list"),
                        ncod = NULL, 
                        ploidy = 2, 
                        sep.in, 
                        sep.out,
                        chk.names = TRUE,
                        chk.plocod = TRUE) {
  
 input <- match.arg(input)
 output <- match.arg(output)
 
 # none sep in default
 if(missing(sep.in)) {
   sep.in <- ""
 }
 
 if(missing(sep.out)) {
   sep.out <- ""
 }
 
 inout <- c("matrix", "alleles.matrix", "list", "alleles.list")
 infile <- match(input, inout)
 outfile <- match(output, inout)
 
 # check that format is matrix for non list cases
 
 f.data <- c("loc", "al", "list", "listal")
 
 f.data.in <- f.data[infile]
 f.data.out <- f.data[outfile]
 
 usefun <- paste("int.", f.data.in, "2", f.data.out, sep = "")
 
 out <- do.call(usefun, list(X = X, ncod = ncod, 
                             ploidy = ploidy, 
                             sep.in = sep.in, 
                             sep.out = sep.out,
                             chk.names = chk.names,
                             chk.plocod = chk.plocod))
 
 out
 
})