outputAnnotationParamsCSV,peakPantheRAnnotation-method {peakPantheR} | R Documentation |
Save annotation parameters (ROI, uROI and FIR) to disk as a CSV file for editing
## S4 method for signature 'peakPantheRAnnotation' outputAnnotationParamsCSV( object, saveFolder, verbose, noSave )
object |
(peakPantheRAnnotation) Annotated peakPantheRAnnotation object |
saveFolder |
(str) Path of folder where annotationParameters_summary.csv will be saved |
verbose |
(bool) If TRUE message progress |
noSave |
(bool) If TRUE the resulting table will be returned without saving to disk |
None
## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted ## compounds # Paths to spectra files spectraPaths <- c('./path/file1', './path/file2', './path/file3') # targetFeatTable targetFeatTable <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), c('cpdID','cpdName','rtMin','rt','rtMax','mzMin','mz', 'mzMax'))), stringsAsFactors=FALSE) targetFeatTable[1,] <- c('ID-1', 'Cpd 1', 3310., 3344.888, 3390., 522.194778, 522.2, 522.205222) targetFeatTable[2,] <- c('ID-2', 'Cpd 2', 3280., 3385.577, 3440., 496.195038, 496.2, 496.204962) targetFeatTable[,c(3:8)] <- vapply(targetFeatTable[,c(3:8)], as.numeric, FUN.VALUE=numeric(2)) emptyAnnotation <- peakPantheRAnnotation(spectraPaths=spectraPaths, targetFeatTable=targetFeatTable) # temporary file savePath <- tempdir() # statistics of an empty annotation outputAnnotationParamsCSV(emptyAnnotation, saveFolder=savePath, verbose=TRUE)