Function reference • peakPantheR

Exported Functions Functions exported by peakPantheR
`peakPantheR` `_PACKAGE` `peakPantheR-package`	peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments
`peakPantheR_start_GUI()`	peakPantheR Graphical User Interface
`peakPantheR_singleFileSearch()`	Search, integrate and report targeted features in a raw spectra
`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
peakPantheRAnnotation object Accessors Accessors
`peakPantheRAnnotation()` `peakPantheRAnnotation()`	An S4 class to represent peakPantheR annotation results
`cpdID(<peakPantheRAnnotation>)`	cpdID accessor
`cpdName(<peakPantheRAnnotation>)`	cpdName accessor
`ROI(<peakPantheRAnnotation>)`	ROI accessor returns targetFeatTable with cpdID, cpdName added
`uROI(<peakPantheRAnnotation>)`	uROI accessor returns targetFeatTable with cpdID, cpdName added
`FIR(<peakPantheRAnnotation>)`	FIR accessor returns targetFeatTable with cpdID, cpdName added
`filepath(<peakPantheRAnnotation>)`	filepath accessor
`cpdMetadata(<peakPantheRAnnotation>)`	cpdMetadata accessor
`spectraMetadata(<peakPantheRAnnotation>)`	spectraMetadata accessor
`acquisitionTime(<peakPantheRAnnotation>)`	acquisitionTime accessor returns value as.POSIXct
`uROIExist(<peakPantheRAnnotation>)`	uROIExist accessor
`useUROI(<peakPantheRAnnotation>)`	useUROI accessor
`useFIR(<peakPantheRAnnotation>)`	useFIR accessor
`TIC(<peakPantheRAnnotation>)`	TIC accessor
`peakTables(<peakPantheRAnnotation>)`	peakTables accessor with cpdID and cpdName added back
`dataPoints(<peakPantheRAnnotation>)`	dataPoints accessor
`peakFit(<peakPantheRAnnotation>)`	peakFit accessor
`isAnnotated(<peakPantheRAnnotation>)`	isAnnotated accessor
`nbSamples(<peakPantheRAnnotation>)`	nbSamples accessor established on filepath
`nbCompounds(<peakPantheRAnnotation>)`	nbCompounds accessor established on cpdID
`annotationTable(<peakPantheRAnnotation>)`	annotationTable accessor
`EICs(<peakPantheRAnnotation>)`	EICs accessor
`filename(<peakPantheRAnnotation>)`	filename accessor by spliting filepath
peakPantheRAnnotation object Methods Methods
`[`(<peakPantheRAnnotation>,<ANY>,<ANY>,<ANY>)	extract parts of peakPantheRAnnotation class
`annotationParamsDiagnostic(<peakPantheRAnnotation>)`	Set uROI and FIR based on annotation results
`outputAnnotationParamsCSV(<peakPantheRAnnotation>)`	Save annotation parameters as CSV
`annotationDiagnosticPlots(<peakPantheRAnnotation>)`	Generate fit diagnostic plots
`outputAnnotationDiagnostic(<peakPantheRAnnotation>)`	Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compound
`outputAnnotationResult(<peakPantheRAnnotation>)`	Save to disk all annotation results as csv files
`resetAnnotation(<peakPantheRAnnotation>)`	Reset a peakPantheRAnnotation and alter samples and compounds information
`resetFIR(<peakPantheRAnnotation>)`	Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if `uROIExist=FALSE`)
`retentionTimeCorrection(<peakPantheRAnnotation>)`	Apply retention time correction methods to adjust the retention time information in the uROI of peakPantheRAnnotation object
Internals Internal functions and helpers
`extractSignalRawData()`	Extract signal in a multiple defined mz rt window from a raw data file
`generateIonChromatogram()`	Generate ion chromatogram from raw data points
`findTargetFeatures()`	Find and integrate target features in each ROI
`fitCurve()`	Curve fitting using minpack.lm
`is.peakPantheR_curveFit()`	Check if object is of class peakPantheR_curveFit
`annotationDiagnosticMultiplot()`	Generate a multiplot of all diagnostic plots
`getAcquisitionDatemzML()`	Parse acquisition date from a mzML file
`getTargetFeatureStatistic()`	Calculate chromatographic peak properties
`integrateFIR()`	Integrate fallback integration regions
`plotEICDetectedPeakwidth()`	Plot samples raw data and detected feature for a single ROI
`plotHistogram()`	Plot variable histogram and density
`predictCurve()`	Predict curve values
`saveSingleFileMultiEIC()`	Save to disk a plot of all ROI EIC and detected feature range
`prepare_advanced_target_parameters()`	Process target region parameters (with uROI, FIR) for object initialisation
`prepare_basic_target_parameters()`	Process target region parameters (simple format) for object initialisation
`peakPantheR_applyRTCorrection()`	Correct targeted retention time based on reference compounds
`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
`emgGaussian_guess()`	Guess function for initial exponentially modified gaussian parameters and bounds
`emgGaussian_minpack.lm()`	Implementation of the Exponentially Modified Gaussian (EMG) peak shape for use with minpack.lm
`emgGaussian_minpack.lm_objectiveFun()`	Exponentially Modified Gaussian minpack.lm objective function
`gaussian_cerf()`	Gaussian Error function
`gaussian_erf()`	Gaussian Error function
`initialise_annotation_from_files_UI_helper()`	UI data import helper - initialise new annotation from files
`spectraPaths_and_metadata_UI_helper()`	UI data import helper - prepare file paths and metadata
`load_annotation_from_file_UI_helper()`	UI data import helper - check loaded annotation
`annotation_showMethod_UI_helper()`	UI show annotation helper - list of properties
`annotation_showText_UI_helper()`	UI show annotation helper - UI sidebar string
`annotation_diagnostic_multiplot_UI_helper()`	UI diagnostic plot helper - single feature multiplot
`annotation_fit_summary_UI_helper()`	UI diagnostic table - fit summary
`outputAnnotationSpectraMetadata_UI_helper()`	UI export helper - spectra path and metadata
`outputAnnotationFeatureMetadata_UI_helper()`	UI export helper - feature metadata
`spectra_metadata_colourScheme_UI_helper()`	UI export plot helper - sample colour

Reference

Exported Functions

peakPantheRAnnotation object Accessors

peakPantheRAnnotation object Methods

Internals