max/ourMELONS
1
0
Fork 0
Code Issues 1 Pull requests Projects Releases Packages Wiki Activity Actions

greedyMix changed to channel data load (close #16)

Browse source
This commit is contained in:
Waldir Leoncio 2021-09-03 08:43:37 +02:00
parent 2ada115bf3
commit a296f9f8fb
2 changed files with 23 additions and 29 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

35
R/greedyMix.R
View file

@ -1,20 +1,23 @@
#' @title Clustering of individuals
#' @param tietue File
#' @param format Format of the data ("BAPS", "GenePop" or "Preprocessed")
#' @param savePreProcessed Save the pre-processed data?
#' @param filePreProcessed Is the file already processed?
#' @param data data file
#' @param format Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")
#' @importFrom utils read.delim
#' @export
greedyMix <- function(
tietue,
format = NULL,
savePreProcessed = NULL,
filePreProcessed = NULL
) {
stop(
"greedyMix() has been superseded by load_fasta().",
" Please change your code to use the latter instead of the former.",
" If you believe the error is internal to rBAPS, please open",
" a new issue (link on the package DESCRIPTION file)."
)
greedyMix <- function(data, format) {
format <- tolower(format)
if (format == "fasta") {
out <- load_fasta(data)
} else if (format == "vcf") {
stop("VCF files not yet supported." )
# TODO #16: implement load_vcf()
} else if (format == "sam") {
stop("SAM files not yet supported." )
# TODO #16: implement load_sam()
} 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}
\title{Clustering of individuals}
\usage{
greedyMix(
tietue,
format = NULL,
savePreProcessed = NULL,
filePreProcessed = NULL
)
greedyMix(data, format)
}
\arguments{
\item{tietue}{File}
\item{data}{data file}
\item{format}{Format of the data ("BAPS", "GenePop" or "Preprocessed")}
\item{savePreProcessed}{Save the pre-processed data?}
\item{filePreProcessed}{Is the file already processed?}
\item{format}{Format of the data c("FASTA", "VCF" ,"SAM", or "GenePop")}
}
\description{
Clustering of individuals