Man pages for phenomecentre/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 |
| annotation_diagnostic_multiplot_UI_helper | UI diagnostic plot helper - single feature multiplot |
| annotationDiagnosticPlots-peakPantheRAnnotation-method | Generate fit diagnostic plots |
| annotation_fit_summary_UI_helper | UI diagnostic table - fit summary |
| annotationParamsDiagnostic-peakPantheRAnnotation-method | Set uROI and FIR based on annotation results |
| annotation_showMethod_UI_helper | UI show annotation helper - list of properties |
| annotation_showText_UI_helper | UI show annotation helper - UI sidebar string |
| 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 |
| EICs-peakPantheRAnnotation-method | EICs accessor |
| emgGaussian_guess | Guess function for initial exponentially modified gaussian... |
| emgGaussian_minpack.lm | Implementation of the Exponentially Modified Gaussian (EMG)... |
| emgGaussian_minpack.lm_objectiveFun | Exponentially Modified Gaussian minpack.lm objective function |
| 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 |
| gaussian_cerf | Gaussian Error function |
| gaussian_erf | Gaussian Error function |
| generateIonChromatogram | Generate ion chromatogram from raw data points |
| getAcquisitionDatemzML | Parse acquisition date from a mzML file |
| getTargetFeatureStatistic | Calculate chromatographic peak properties |
| initialise_annotation_from_files_UI_helper | UI data import helper - initialise new annotation from files |
| integrateFIR | Integrate fallback integration regions |
| isAnnotated-peakPantheRAnnotation-method | isAnnotated accessor |
| is.peakPantheR_curveFit | Check if object is of class peakPantheR_curveFit |
| load_annotation_from_file_UI_helper | UI data import helper - check loaded annotation |
| 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... |
| outputAnnotationFeatureMetadata_UI_helper | UI export helper - feature metadata |
| outputAnnotationParamsCSV-peakPantheRAnnotation-method | Save annotation parameters as CSV |
| outputAnnotationResult-peakPantheRAnnotation-method | Save to disk all annotation results as csv files |
| outputAnnotationSpectraMetadata_UI_helper | UI export helper - spectra path and metadata |
| 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_applyRTCorrection | Correct targeted retention time based on reference compounds |
| peakPantheR_loadAnnotationParamsCSV | Load fit parameters from CSV |
| peakPantheR_parallelAnnotation | Search, integrate and report targeted features in a multiple... |
| 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... |
| peakPantheR_quickEIC | Extract and plot a EIC from a raw data file |
| peakPantheR_ROIStatistics | Save to disk each ROI EIC and mean IS RT |
| peakPantheR_singleFileSearch | Search, integrate and report targeted features in a raw... |
| peakPantheR_start_GUI | peakPantheR Graphical User Interface |
| 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 |
| prepare_advanced_target_parameters | Process target region parameters (with uROI, FIR) for object... |
| prepare_basic_target_parameters | Process target region parameters (simple format) for object... |
| resetAnnotation-peakPantheRAnnotation-method | Reset a peakPantheRAnnotation and alter samples and compounds... |
| resetFIR-peakPantheRAnnotation-method | Reset FIR windows to uROI or ROI values Reset FIR windows to... |
| retentionTimeCorrection-peakPantheRAnnotation-method | Apply retention time correction methods to adjust the... |
| 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 |
| spectra_metadata_colourScheme_UI_helper | UI export plot helper - sample colour |
| spectraMetadata-peakPantheRAnnotation-method | spectraMetadata accessor |
| spectraPaths_and_metadata_UI_helper | UI data import helper - prepare file paths and metadata |
| 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 |
