outputAnnotationResult,peakPantheRAnnotation-method {peakPantheR} | R Documentation

## Save to disk all annotation results as csv files

### Description

Save to disk all annotation results as `annotationName_ ... .csv` files: compound metadata (`cpdMetadata`, `cpdID`, `cpdName`) and spectra metadata (`spectraMetadata`, `acquisitionTime`, `TIC`), summary of fit (ratio of peaks found: `ratio_peaks_found`, ratio of peaks filled: `ratio_peaks_filled`, mean ppm_error: `ppm_error`, mean rt_dev_sec: `rt_dev_sec`), and a file for each column of `peakTables` (with samples as rows and compounds as columns)

### Usage

    ## S4 method for signature 'peakPantheRAnnotation'
    outputAnnotationResult(
        object,
        saveFolder,
        annotationName = "annotationResult",
        verbose = TRUE
    )

### Arguments

`object` | (peakPantheRAnnotation) Annotated peakPantheRAnnotation object
`saveFolder` | (str) Path of folder where the annotation result csv will be saved
`annotationName` | (str) name of annotation to use in the saved csv
`verbose` | (bool) If TRUE message progress

### Value

None

### Examples

    if(requireNamespace('faahKO')){
    ## Initialise a peakPantheRAnnotation object with 3 samples and 2 targeted
    ## compounds

    # Paths to spectra files
    library(faahKO)
    spectraPaths <- c(system.file('cdf/KO/ko15.CDF', package = 'faahKO'),
                        system.file('cdf/KO/ko16.CDF', package = 'faahKO'),
                        system.file('cdf/KO/ko18.CDF', package = 'faahKO'))

    # 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)

    # Calculate annotation
    annotation      <- peakPantheR_parallelAnnotation(emptyAnnotation, ncores=0,
                                    getAcquTime=FALSE, verbose=FALSE)$annotation

    # temporary location
    savePath1       <- tempdir()
    outputAnnotationResult(annotation, saveFolder=savePath1,
                            annotationName='testProject', verbose=TRUE)
    }

[Package peakPantheR version 1.4.0 Index]