Nothing
PeakML.Methods.getRawDataPaths <- function(PeakMLtree, Rawpath = NULL){
# PRE:
# PeakMLtree, path of raw files if different from the ones referened in the peakml files
# POST:
# Return the samples names and the full path to where the .mzXML files are located
sampleNames <- sapply(getNodeSet(PeakMLtree,"/peakml/header/measurements/measurement/label"),xmlValue)
folders <- sapply(getNodeSet(PeakMLtree,"/peakml/header/measurements/measurement/files/file/location"),xmlValue)
filenames <- sapply(getNodeSet(PeakMLtree,"/peakml/header/measurements/measurement/files/file/name"),xmlValue)
peakmlfiles <- grep(".peakml",filenames)
if (length(peakmlfiles)!=0)
{
folders <- folders[-c(peakmlfiles)]
filenames <- filenames[-c(peakmlfiles)]
}
if (!is.null(Rawpath)){
dirContent <- dir(Rawpath, recursive = TRUE, full.names=TRUE)
fileid <- rep(NA,length(sampleNames))
for (filenum in 1:length(sampleNames))
{
hit <- grep (filenames[filenum],dirContent, fixed=TRUE)
if (length(hit)!=0)
{
fileid[filenum] <- hit[1]
}
}
if(length(which(is.na(fileid)))==0){
rawDataPaths <- dirContent[fileid]
cat(paste("Raw data file located at: ", rawDataPaths, "\n", sep=""))
} else{
cat(paste("Raw data file: ",sampleNames[which(is.na(fileid))],"cant't be found in folder: ", Rawpath, "\n", sep=""))
rawDataPaths <- NULL
}
} else{
rawDataPaths <- paste(folders,filenames,sep="/")
mzFiles <- which(file.exists(rawDataPaths)==TRUE)
if (length(mzFiles) == length(rawDataPaths)){
cat(paste("Raw data file located at: ", rawDataPaths, "\n", sep=""))
} else {
cat(paste("Raw data file can't be read from location': ", rawDataPaths, "\n", sep=""))
rawDataPaths <- NULL
}
}
list(sampleNames,rawDataPaths)
}
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