EICs,peakPantheRAnnotation-method
                        EICs accessor
FIR,peakPantheRAnnotation-method
                        FIR accessor returns targetFeatTable with
                        cpdID, cpdName added
ROI,peakPantheRAnnotation-method
                        ROI accessor returns targetFeatTable with
                        cpdID, cpdName added
TIC,peakPantheRAnnotation-method
                        TIC accessor
[,peakPantheRAnnotation,ANY,ANY,ANY-method
                        extract parts of peakPantheRAnnotation class
acquisitionTime,peakPantheRAnnotation-method
                        acquisitionTime accessor returns value
                        as.POSIXct
annotationDiagnosticMultiplot
                        Generate a multiplot of all diagnostic plots
annotationDiagnosticPlots,peakPantheRAnnotation-method
                        Generate fit diagnostic plots Generate fit
                        diagnostic plots for each ROI: 'EICFit' the raw
                        data and detected feature fit,
                        'rtPeakwidthVert' detected peaks retention time
                        apex and peakwidth (vertical and no run order),
                        'rtPeakwidthHorzRunOrder' detected peaks
                        retention time apex and peakwidth by run order,
                        'mzPeakwidthHorzRunOrder' detected peaks m/z
                        apex and peakwidth by run order, 'areaRunOrder'
                        detected peaks area by run order, 'rtHistogram'
                        histogram of detected peaks retention time,
                        'mzHistogram' histogram of detected peaks m/z,
                        'areaHistogram' histogram of detected peaks
                        area.
annotationParamsDiagnostic,peakPantheRAnnotation-method
                        Set uROI and FIR based on annotation results
                        Set updated ROI (uROI) and Fallback Integration
                        Regions (FIR) based on the annotation results.
                        If the object is not annotated, it is returned
                        untouched. ROI is not modified. If uROI exist
                        they are left untouched, otherwise they are set
                        as the minimum and maximum found peaks limits
                        (+/-5% of ROI in retention time). If FIR are
                        used they are left untouched, otherwise they
                        are set as the median of the found limits
                        (rtMin, rtMax, mzMin, mzMax).
annotationTable,peakPantheRAnnotation-method
                        annotationTable accessor annotationTable
                        returns a dataframe (row samples, col
                        compounds) filled with a specific peakTable
                        column
cpdID,peakPantheRAnnotation-method
                        cpdID accessor
cpdMetadata,peakPantheRAnnotation-method
                        cpdMetadata accessor
cpdName,peakPantheRAnnotation-method
                        cpdName accessor
dataPoints,peakPantheRAnnotation-method
                        dataPoints accessor
extractSignalRawData    Extract signal in a multiple defined mz rt
                        window from a raw data file
filename,peakPantheRAnnotation-method
                        filename accessor by spliting filepath
filepath,peakPantheRAnnotation-method
                        filepath accessor
findTargetFeatures      Find and integrate target features in each ROI
fitCurve                Curve fitting using minpack.lm
generateIonChromatogram
                        Generate ion chromatogram from raw data points
getAcquisitionDatemzML
                        Parse acquisition date from a mzML file
getTargetFeatureStatistic
                        Calculate chromatographic peak properties
integrateFIR            Integrate fallback integration regions
is.peakPantheR_curveFit
                        Check if object is of class
                        peakPantheR_curveFit
isAnnotated,peakPantheRAnnotation-method
                        isAnnotated accessor
nbCompounds,peakPantheRAnnotation-method
                        nbCompounds accessor established on cpdID
nbSamples,peakPantheRAnnotation-method
                        nbSamples accessor established on filepath
outputAnnotationDiagnostic,peakPantheRAnnotation-method
                        Save to disk the annotation parameters as CSV
                        and a diagnostic plot per fitted compound Save
                        to disk the annotation parameters as CSV (as
                        generated by 'outputAnnotationParamsCSV()') and
                        a diagnostic plot per fitted compound (as
                        generated by 'annotationDiagnosticMultiplot()')
                        if 'savePlots' is TRUE
outputAnnotationParamsCSV,peakPantheRAnnotation-method
                        Save annotation parameters as CSV Save
                        annotation parameters (ROI, uROI and FIR) to
                        disk as a CSV file for editing
outputAnnotationResult,peakPantheRAnnotation-method
                        Save to disk all annotation results as csv
                        files 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)
peakFit,peakPantheRAnnotation-method
                        peakFit accessor
peakPantheR             peakPantheR: A package for Peak Picking and
                        ANnoTation of High resolution Experiments
peakPantheRAnnotation   An S4 class to represent peakPantheR annotation
                        results
peakPantheR_loadAnnotationParamsCSV
                        Load fit parameters from CSV
peakPantheR_parallelAnnotation
                        Search, integrate and report targeted features
                        in a multiple spectra
peakPantheR_singleFileSearch
                        Search, integrate and report targeted features
                        in a raw spectra
peakTables,peakPantheRAnnotation-method
                        peakTables accessor with cpdID and cpdName
                        added back
plotEICDetectedPeakwidth
                        Plot samples raw data and detected feature for
                        a single ROI
plotEICFit              Plot samples raw data and detected feature for
                        a single ROI
plotHistogram           Plot variable histogram and density
plotPeakwidth           Plot peak value and peakwidth by acquisition
                        time or in input order
predictCurve            Predict curve values
resetAnnotation,peakPantheRAnnotation-method
                        Reset a peakPantheRAnnotation and alter samples
                        and compounds information 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'.
saveSingleFileMultiEIC
                        Save to disk a plot of all ROI EIC and detected
                        feature range
skew_erf                Gaussian Error function
skewedGaussian_guess    Guess function for initial skewed gaussian
                        parameters and bounds
skewedGaussian_minpack.lm
                        Implementation of the Skewed Gaussian peak
                        shape for use with minpack.lm
skewedGaussian_minpack.lm_objectiveFun
                        Skewed Gaussian minpack.lm objective function
spectraMetadata,peakPantheRAnnotation-method
                        spectraMetadata accessor
uROI,peakPantheRAnnotation-method
                        uROI accessor returns targetFeatTable with
                        cpdID, cpdName added
uROIExist,peakPantheRAnnotation-method
                        uROIExist accessor
useFIR,peakPantheRAnnotation-method
                        useFIR accessor
useUROI,peakPantheRAnnotation-method
                        useUROI accessor
