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
annotationParamsDiagnostic,peakPantheRAnnotation-method
                        Set uROI and FIR based on annotation results
annotationTable,peakPantheRAnnotation-method
                        annotationTable accessor
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
outputAnnotationParamsCSV,peakPantheRAnnotation-method
                        Save annotation parameters as CSV
outputAnnotationResult,peakPantheRAnnotation-method
                        Save to disk all annotation results as csv
                        files
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_ROIStatistics
                        Save to disk each ROI EIC and mean IS RT
peakPantheR_loadAnnotationParamsCSV
                        Load fit parameters from CSV
peakPantheR_parallelAnnotation
                        Search, integrate and report targeted features
                        in a multiple spectra
peakPantheR_plotEICFit
                        Plot samples raw data and detected feature for
                        a single ROI
peakPantheR_plotPeakwidth
                        Plot peak value and peakwidth by acquisition
                        time or in input order
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
plotHistogram           Plot variable histogram and density
predictCurve            Predict curve values
resetAnnotation,peakPantheRAnnotation-method
                        Reset a peakPantheRAnnotation and alter samples
                        and compounds information
resetFIR,peakPantheRAnnotation-method
                        Reset FIR windows to uROI or ROI values Reset
                        FIR windows to uROI (or ROI if
                        'uROIExist=FALSE')
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
