Nothing
newDir<-function(runBATMANDir = getwd(), overwriteFile = FALSE)
{
## written by Dr. Jie Hao, Imperial College London
## create a new directory with installed data files
dirRoot<-paste(runBATMANDir,"/runBATMAN",sep="")
if(!file.exists(dirRoot)) {
dir.create(dirRoot)
}
dirIP<-paste(dirRoot,"/BatmanInput",sep="")
if(!file.exists(dirIP)){
dir.create(dirIP)
}
dirPST<-paste(dirIP,"/PureSpectraTemplate",sep="")
if(!file.exists(dirPST)){
dir.create(dirPST)
}
extdir<-system.file("extdata",package="batman")
dirRastGln<-paste(extdir,"/PureSpectraTemplate/L-Glutamine.txt",sep="")
cp<-file.copy(dirRastGln,dirPST,overwrite=overwriteFile)
## dirTPure<-paste(dirIP,"/testBrukerPureSpecForRasterTemplate",sep="")
## if(!file.exists(dirTPure)){
## dir.create(dirTPure)
## }
## dirTPure1<-paste(dirTPure,"/testPure1",sep="")
## if(!file.exists(dirTPure1)){
## dir.create(dirTPure1)
## }
dirOP<-paste(dirRoot,"/BatmanOutput",sep="")
if(!file.exists(dirOP)) {
dir.create(dirOP)
}
## src.dir <- paste(extdir,"/testBrukerPureSpecForRasterTemplate/testPure1",sep="")
## dest.dir <-dirTPure1
## file.names <- dir(src.dir)
## sapply(file.names, function(x) {
## file.copy(from=paste(src.dir, x, sep="/"),
## to=paste(dest.dir, x, sep="/"),
## overwrite = FALSE) })
dirbo<-paste(extdir,"/batmanOptions.txt",sep="")
cp<-file.copy(dirbo,dirIP, overwrite=overwriteFile)
dird<-paste(extdir,"/NMRdata.txt",sep="")
cp<-file.copy(dird,dirIP, overwrite=overwriteFile)
dirL<-paste(extdir,"/metabolitesList.csv",sep="")
cp<-file.copy(dirL,dirIP, overwrite=overwriteFile)
dirR<-paste(extdir,"/multi_data.csv",sep="")
cp<-file.copy(dirR,dirIP,overwrite=overwriteFile)
dirRU<-paste(extdir,"/multi_data_user.csv",sep="")
cp<-file.copy(dirRU,dirIP,overwrite=overwriteFile)
dirRU_adj<-paste(extdir,"/multi_data_user_adj.csv",sep="")
cp<-file.copy(dirRU_adj,dirIP,overwrite=overwriteFile)
dirA<-c(dirRoot, dirIP, dirOP, dirPST)
return (dirA)
}
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