Man pages for peakPantheR
Peak Picking and Annotation of High Resolution Experiments
| 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... |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | Set uROI and FIR based on annotation results Set updated ROI... |
| annotationTable-peakPantheRAnnotation-method | annotationTable accessor annotationTable returns a dataframe... |
| cpdID-peakPantheRAnnotation-method | cpdID accessor |
| cpdMetadata-peakPantheRAnnotation-method | cpdMetadata accessor |
| cpdName-peakPantheRAnnotation-method | cpdName accessor |
| dataPoints-peakPantheRAnnotation-method | dataPoints accessor |
| EICs-peakPantheRAnnotation-method | EICs accessor |
| extractSignalRawData | Extract signal in a multiple defined mz rt window from a raw... |
| filename-peakPantheRAnnotation-method | filename accessor by spliting filepath |
| filepath-peakPantheRAnnotation-method | filepath accessor |
| findTargetFeatures | Find and integrate target features in each ROI |
| FIR-peakPantheRAnnotation-method | FIR accessor returns targetFeatTable with cpdID, cpdName... |
| 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 |
| isAnnotated-peakPantheRAnnotation-method | isAnnotated accessor |
| is.peakPantheR_curveFit | Check if object is of class peakPantheR_curveFit |
| 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... |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | Save annotation parameters as CSV Save annotation parameters... |
| outputAnnotationResult-peakPantheRAnnotation-method | Save to disk all annotation results as csv files Save to disk... |
| peakFit-peakPantheRAnnotation-method | peakFit accessor |
| peakPantheR | peakPantheR: A package for Peak Picking and ANnoTation of... |
| 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... |
| peakPantheR_singleFileSearch | Search, integrate and report targeted features in a raw... |
| 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... |
| predictCurve | Predict curve values |
| resetAnnotation-peakPantheRAnnotation-method | Reset a peakPantheRAnnotation and alter samples and compounds... |
| ROI-peakPantheRAnnotation-method | ROI accessor returns targetFeatTable with cpdID, cpdName... |
| saveSingleFileMultiEIC | Save to disk a plot of all ROI EIC and detected feature range |
| skewedGaussian_guess | Guess function for initial skewed gaussian parameters and... |
| skewedGaussian_minpack.lm | Implementation of the Skewed Gaussian peak shape for use with... |
| skewedGaussian_minpack.lm_objectiveFun | Skewed Gaussian minpack.lm objective function |
| skew_erf | Gaussian Error function |
| spectraMetadata-peakPantheRAnnotation-method | spectraMetadata accessor |
| sub-peakPantheRAnnotation-ANY-ANY-ANY-method | extract parts of peakPantheRAnnotation class |
| TIC-peakPantheRAnnotation-method | TIC accessor |
| uROIExist-peakPantheRAnnotation-method | uROIExist accessor |
| uROI-peakPantheRAnnotation-method | uROI accessor returns targetFeatTable with cpdID, cpdName... |
| useFIR-peakPantheRAnnotation-method | useFIR accessor |
| useUROI-peakPantheRAnnotation-method | useUROI accessor |
