outputAnnotationParamsCSV-peakPantheRAnnotation-method: Save annotation parameters as CSV

In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments

Save annotation parameters as CSV

Description

Save annotation parameters (ROI, uROI and FIR) to disk as a CSV file for editing

Usage

## S4 method for signature 'peakPantheRAnnotation'
outputAnnotationParamsCSV(
    object,
    saveFolder,
    verbose,
    noSave
)

Arguments

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

Value

None

Examples

## 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)

phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.