15f2cbcf08
Current one from https://genome.sph.umich.edu/wiki/SAM. Readable by the "VladaMilch/pdProbeRemap" package.
24 lines
No EOL
772 B
R
24 lines
No EOL
772 B
R
#' @title Clustering of individuals
|
|
#' @param data data file
|
|
#' @param format Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")
|
|
#' @param verbose if \code{TRUE}, prints extra output information
|
|
#' @importFrom utils read.delim
|
|
#' @importFrom vcfR read.vcfR
|
|
#' @export
|
|
greedyMix <- function(data, format, verbose = TRUE) {
|
|
format <- tolower(format)
|
|
if (format == "fasta") {
|
|
out <- load_fasta(data)
|
|
} else if (format == "vcf") {
|
|
out <- vcfR::read.vcfR(data, verbose = verbose)
|
|
} else if (format == "sam") {
|
|
stop("SAM files not yet supported." )
|
|
# TODO #18: implement load_sam()
|
|
} else if (format == "genepop") {
|
|
# TODO #19: implement load_genepop()
|
|
stop("GenePop files not yet supported." )
|
|
} else {
|
|
stop("Format not supported.")
|
|
}
|
|
return(out)
|
|
} |