resetAnnotation,peakPantheRAnnotation-method {peakPantheR} | R Documentation

## Reset a peakPantheRAnnotation and alter samples and compounds information

### Description

Reset a peakPantheRAnnotation (remove results and set `isAnnotated=FALSE`). If a different number of samples ( `spectraPaths`) or compounds (`targetFeatTable`) are passed, the object will be initialised to the new size. For input values left as NULL, the slots (`filepath` (from `spectraPaths`), `ROI`, `cpdID`, `cpdName` (from `targetFeatTable`), `uROI`, `FIR`, `cpdMetadata`, `spectraMetadata`, `uROIExist`, `useUROI` and `useFIR`) will be filled with values from `previousAnnotation`.

### Usage

    ## S4 method for signature 'peakPantheRAnnotation'
    resetAnnotation(
        previousAnnotation,
        spectraPaths = NULL,
        targetFeatTable = NULL,
        uROI = NULL,
        FIR = NULL,
        cpdMetadata = NULL,
        spectraMetadata = NULL,
        uROIExist = NULL,
        useUROI = NULL,
        useFIR = NULL,
        verbose = TRUE,
        ...
    )

### Arguments

`previousAnnotation` | (peakPantheRAnnotation) object to reset
`spectraPaths` | NULL or a character vector of spectra file paths, to set samples to process
`targetFeatTable` | NULL or a `data.frame` of compounds to target as rows and parameters as columns: `cpdID` (str), `cpdName` (str), `rtMin` (float in seconds), `rt` (float in seconds, or NA), `rtMax` (float in seconds), `mzMin` (float), `mz` (float or NA), `mzMax` (float). Set compounds to target.
`uROI` | NULL or a data.frame of updated Regions Of Interest (uROI) with compounds as row and uROI parameters as columns: `rtMin` (float in seconds), `rt` (float in seconds, or NA), `rtMax` (float in seconds), `mzMin` (float), `mz` (float or NA), `mzMax` (float).
`FIR` | NULL or a data.frame of Fallback Integration Regions (FIR) with compounds as row and FIR parameters as columns: `rtMin` (float in seconds), `rtMax` (float in seconds), `mzMin` (float), `mzMax` (float).
`cpdMetadata` | NULL or a data.frame of compound metadata, with compounds as row and metadata as columns
`spectraMetadata` | NULL or a data.frame of sample metadata, with samples as row and metadata as columns
`uROIExist` | NULL or a logical stating if uROI have been set
`useUROI` | NULL or a logical stating if uROI are to be used
`useFIR` | NULL or a logical stating if FIR are to be used
`verbose` | (bool) If TRUE message progress
`...` | Additional slots and values to set when resetting the object (`cpdID`, `cpdName`, `ROI`, `filepath`, `TIC`, `acquisitionTime`, `peakTables`, `dataPoints`, `peakFit`)

### Value

(peakPantheRAnnotation) object reset with previous results removed and slots updated

### 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'))

    # 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))

    smallAnnotation  <- peakPantheRAnnotation(spectraPaths=spectraPaths,
                                            targetFeatTable=targetFeatTable)
    smallAnnotation
    # An object of class peakPantheRAnnotation
    #  2 compounds in 2 samples.
    #  updated ROI do not exist (uROI)
    #  does not use updated ROI (uROI)
    #  does not use fallback integration regions (FIR)
    #  is not annotated

    # Reset and change number of spectra
    newSpectraPaths  <- 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'))
    largerAnnotation <- resetAnnotation(smallAnnotation,
                                        spectraPaths=newSpectraPaths,
                                        verbose=TRUE)
    largerAnnotation
    # An object of class peakPantheRAnnotation
    #  2 compounds in 3 samples.
    #  updated ROI do not exist (uROI)
    #  does not use updated ROI (uROI)
    #  does not use fallback integration regions (FIR)
    #  is not annotated
    }

[Package peakPantheR version 1.4.0 Index]