Description Usage Arguments Value Examples
Save annotation parameters (ROI, uROI and FIR) to disk as a CSV file for editing
1 2 3 4 5 6 7 | ## 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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## 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)
|
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