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greedyMix changed to channel data load (close #16)

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Waldir Leoncio 2021-09-03 08:43:37 +02:00
parent 2ada115bf3
commit a296f9f8fb
2 changed files with 23 additions and 29 deletions
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35
R/greedyMix.R
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@ -1,20 +1,23 @@
#' @title Clustering of individuals #' @title Clustering of individuals
#' @param tietue File #' @param data data file
#' @param format Format of the data ("BAPS", "GenePop" or "Preprocessed") #' @param format Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")
#' @param savePreProcessed Save the pre-processed data?
#' @param filePreProcessed Is the file already processed?
#' @importFrom utils read.delim #' @importFrom utils read.delim
#' @export #' @export
greedyMix <- function( greedyMix <- function(data, format) {
tietue, format <- tolower(format)
format = NULL, if (format == "fasta") {
savePreProcessed = NULL, out <- load_fasta(data)
filePreProcessed = NULL } else if (format == "vcf") {
) { stop("VCF files not yet supported." )
stop( # TODO #16: implement load_vcf()
"greedyMix() has been superseded by load_fasta().", } else if (format == "sam") {
" Please change your code to use the latter instead of the former.", stop("SAM files not yet supported." )
" If you believe the error is internal to rBAPS, please open", # TODO #16: implement load_sam()
" a new issue (link on the package DESCRIPTION file)." } else if(format == "genepop") {
) # TODO #16: implement load_genepop()
stop("GenePop files not yet supported." )
} else {
stop("Format not supported.")
}
return(out)
} }

15
man/greedyMix.Rd
View file

@ -4,21 +4,12 @@
\alias{greedyMix} \alias{greedyMix}
\title{Clustering of individuals} \title{Clustering of individuals}
\usage{ \usage{
greedyMix( greedyMix(data, format)
tietue,
format = NULL,
savePreProcessed = NULL,
filePreProcessed = NULL
)
} }
\arguments{ \arguments{
\item{tietue}{File} \item{data}{data file}
\item{format}{Format of the data ("BAPS", "GenePop" or "Preprocessed")} \item{format}{Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")}
\item{savePreProcessed}{Save the pre-processed data?}
\item{filePreProcessed}{Is the file already processed?}
} }
\description{ \description{
Clustering of individuals Clustering of individuals