Man pages for phenomecentre/peakPantheR
Peak Picking and Annotation of High Resolution Experiments

acquisitionTime-peakPantheRAnnotation-methodacquisitionTime accessor returns value as.POSIXct
annotationDiagnosticMultiplotGenerate a multiplot of all diagnostic plots
annotationDiagnosticPlots-peakPantheRAnnotation-methodGenerate fit diagnostic plots Generate fit diagnostic plots...
annotationParamsDiagnostic-peakPantheRAnnotation-methodSet uROI and FIR based on annotation results Set updated ROI...
annotationTable-peakPantheRAnnotation-methodannotationTable accessor annotationTable returns a dataframe...
cpdID-peakPantheRAnnotation-methodcpdID accessor
cpdMetadata-peakPantheRAnnotation-methodcpdMetadata accessor
cpdName-peakPantheRAnnotation-methodcpdName accessor
dataPoints-peakPantheRAnnotation-methoddataPoints accessor
EICs-peakPantheRAnnotation-methodEICs accessor
extractSignalRawDataExtract signal in a multiple defined mz rt window from a raw...
filename-peakPantheRAnnotation-methodfilename accessor by spliting filepath
filepath-peakPantheRAnnotation-methodfilepath accessor
findTargetFeaturesFind and integrate target features in each ROI
FIR-peakPantheRAnnotation-methodFIR accessor returns targetFeatTable with cpdID, cpdName...
fitCurveCurve fitting using minpack.lm
generateIonChromatogramGenerate ion chromatogram from raw data points
getAcquisitionDatemzMLParse acquisition date from a mzML file
getTargetFeatureStatisticCalculate chromatographic peak properties
integrateFIRIntegrate fallback integration regions
isAnnotated-peakPantheRAnnotation-methodisAnnotated accessor
is.peakPantheR_curveFitCheck if object is of class peakPantheR_curveFit
nbCompounds-peakPantheRAnnotation-methodnbCompounds accessor established on cpdID
nbSamples-peakPantheRAnnotation-methodnbSamples accessor established on filepath
outputAnnotationDiagnostic-peakPantheRAnnotation-methodSave to disk the annotation parameters as CSV and a...
outputAnnotationParamsCSV-peakPantheRAnnotation-methodSave annotation parameters as CSV Save annotation parameters...
outputAnnotationResult-peakPantheRAnnotation-methodSave to disk all annotation results as csv files Save to disk...
peakFit-peakPantheRAnnotation-methodpeakFit accessor
peakPantheRpeakPantheR: A package for Peak Picking and ANnoTation of...
peakPantheRAnnotationAn S4 class to represent peakPantheR annotation results
peakPantheR_loadAnnotationParamsCSVLoad fit parameters from CSV
peakPantheR_parallelAnnotationSearch, integrate and report targeted features in a multiple...
peakPantheR_plotEICFitPlot samples raw data and detected feature for a single ROI
peakPantheR_plotPeakwidthPlot peak value and peakwidth by acquisition time or in input...
peakPantheR_ROIStatisticsSave to disk each ROI EIC and mean IS RT Using reference...
peakPantheR_singleFileSearchSearch, integrate and report targeted features in a raw...
peakTables-peakPantheRAnnotation-methodpeakTables accessor with cpdID and cpdName added back
plotEICDetectedPeakwidthPlot samples raw data and detected feature for a single ROI
plotHistogramPlot variable histogram and density
predictCurvePredict curve values
resetAnnotation-peakPantheRAnnotation-methodReset a peakPantheRAnnotation and alter samples and compounds...
ROI-peakPantheRAnnotation-methodROI accessor returns targetFeatTable with cpdID, cpdName...
saveSingleFileMultiEICSave to disk a plot of all ROI EIC and detected feature range
skewedGaussian_guessGuess function for initial skewed gaussian parameters and...
skewedGaussian_minpack.lmImplementation of the Skewed Gaussian peak shape for use with...
skewedGaussian_minpack.lm_objectiveFunSkewed Gaussian minpack.lm objective function
skew_erfGaussian Error function
spectraMetadata-peakPantheRAnnotation-methodspectraMetadata accessor
sub-peakPantheRAnnotation-ANY-ANY-ANY-methodextract parts of peakPantheRAnnotation class
TIC-peakPantheRAnnotation-methodTIC accessor
uROIExist-peakPantheRAnnotation-methoduROIExist accessor
uROI-peakPantheRAnnotation-methoduROI accessor returns targetFeatTable with cpdID, cpdName...
useFIR-peakPantheRAnnotation-methoduseFIR accessor
useUROI-peakPantheRAnnotation-methoduseUROI accessor
phenomecentre/peakPantheR documentation built on Sept. 27, 2018, 2:29 a.m.