outputAnnotationParamsCSV,peakPantheRAnnotation-method {peakPantheR} | R Documentation

## 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)

[Package peakPantheR version 1.4.0 Index]