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| acquisitionTime | acquisitionTime accessor returns value as.POSIXct |
| acquisitionTime-method | acquisitionTime accessor returns value as.POSIXct |
| annotationDiagnosticMultiplot | Generate a multiplot of all diagnostic plots |
| annotationDiagnosticPlots | Generate fit diagnostic plots |
| annotationDiagnosticPlots-method | Generate fit diagnostic plots |
| annotationParamsDiagnostic | Set uROI and FIR based on annotation results |
| annotationParamsDiagnostic-method | Set uROI and FIR based on annotation results |
| annotationTable | annotationTable accessor |
| annotationTable-method | annotationTable accessor |
| cpdID | cpdID accessor |
| cpdID-method | cpdID accessor |
| cpdMetadata | cpdMetadata accessor |
| cpdMetadata-method | cpdMetadata accessor |
| cpdName | cpdName accessor |
| cpdName-method | cpdName accessor |
| dataPoints | dataPoints accessor |
| dataPoints-method | dataPoints accessor |
| EICs | EICs accessor |
| EICs-method | EICs accessor |
| extractSignalRawData | Extract signal in a multiple defined mz rt window from a raw data file |
| filename | filename accessor by spliting filepath |
| filename-method | filename accessor by spliting filepath |
| filepath | filepath accessor |
| filepath-method | filepath accessor |
| findTargetFeatures | Find and integrate target features in each ROI |
| FIR | FIR accessor returns targetFeatTable with cpdID, cpdName added |
| FIR-method | FIR accessor returns targetFeatTable with cpdID, cpdName added |
| 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 | isAnnotated accessor |
| isAnnotated-method | isAnnotated accessor |
| nbCompounds | nbCompounds accessor established on cpdID |
| nbCompounds-method | nbCompounds accessor established on cpdID |
| nbSamples | nbSamples accessor established on filepath |
| nbSamples-method | nbSamples accessor established on filepath |
| outputAnnotationDiagnostic | Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compound |
| outputAnnotationDiagnostic-method | Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compound |
| outputAnnotationParamsCSV | Save annotation parameters as CSV |
| outputAnnotationParamsCSV-method | Save annotation parameters as CSV |
| outputAnnotationResult | Save to disk all annotation results as csv files |
| outputAnnotationResult-method | Save to disk all annotation results as csv files |
| peakFit | peakFit accessor |
| peakFit-method | peakFit accessor |
| peakPantheR | peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments |
| peakpanther | peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments |
| peakPantheRAnnotation | An S4 class to represent peakPantheR annotation results |
| peakPantheRAnnotation-class | 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_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_ROIStatistics | Save to disk each ROI EIC and mean IS RT |
| peakPantheR_singleFileSearch | Search, integrate and report targeted features in a raw spectra |
| peakTables | peakTables accessor with cpdID and cpdName added back |
| peakTables-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 | Reset a peakPantheRAnnotation and alter samples and compounds information |
| resetAnnotation-method | Reset a peakPantheRAnnotation and alter samples and compounds information |
| resetFIR | Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if 'uROIExist=FALSE') |
| resetFIR-method | Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if 'uROIExist=FALSE') |
| ROI | ROI accessor returns targetFeatTable with cpdID, cpdName added |
| ROI-method | ROI accessor returns targetFeatTable with cpdID, cpdName added |
| saveSingleFileMultiEIC | Save to disk a plot of all ROI EIC and detected feature range |
| 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 |
| skew_erf | Gaussian Error function |
| spectraMetadata | spectraMetadata accessor |
| spectraMetadata-method | spectraMetadata accessor |
| TIC | TIC accessor |
| TIC-method | TIC accessor |
| uROI | uROI accessor returns targetFeatTable with cpdID, cpdName added |
| uROI-method | uROI accessor returns targetFeatTable with cpdID, cpdName added |
| uROIExist | uROIExist accessor |
| uROIExist-method | uROIExist accessor |
| useFIR | useFIR accessor |
| useFIR-method | useFIR accessor |
| useUROI | useUROI accessor |
| useUROI-method | useUROI accessor |
| [-method | extract parts of peakPantheRAnnotation class |
| _PACKAGE | peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments |