# Peak Picking and Annotation of High Resolution Experiments

## Documentation for package ‘peakPantheR’ version 1.25.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E F G I L N O P R S T U misc

peakPantheR-package | peakPantheR: A package for Peak Picking and ANnoTation of High resolution Experiments

## -- A --

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
annotation_diagnostic_multiplot_UI_helper | UI diagnostic plot helper - single feature multiplot
annotation_fit_summary_UI_helper | UI diagnostic table - fit summary
annotation_showMethod_UI_helper | UI show annotation helper - list of properties
annotation_showText_UI_helper | UI show annotation helper - UI sidebar string

## -- C --

cpdID | cpdID accessor
cpdID-method | cpdID accessor
cpdMetadata | cpdMetadata accessor
cpdMetadata-method | cpdMetadata accessor
cpdName | cpdName accessor
cpdName-method | cpdName accessor

## -- D --

dataPoints | dataPoints accessor
dataPoints-method | dataPoints accessor

## -- E --

EICs | EICs accessor
EICs-method | EICs accessor
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
extractSignalRawData | Extract signal in a multiple defined mz rt window from a raw data file

## -- F --

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

## -- G --

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

## -- I --

initialise_annotation_from_files_UI_helper | UI data import helper - initialise new annotation from files
integrateFIR | Integrate fallback integration regions
is.peakPantheR_curveFit | Check if object is of class peakPantheR_curveFit
isAnnotated | isAnnotated accessor
isAnnotated-method | isAnnotated accessor

## -- L --

load_annotation_from_file_UI_helper | UI data import helper - check loaded annotation

## -- N --

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

## -- O --

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
outputAnnotationFeatureMetadata_UI_helper | UI export helper - feature metadata
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
outputAnnotationSpectraMetadata_UI_helper | UI export helper - spectra path and metadata

## -- P --

peakFit | peakFit accessor
peakFit-method | peakFit accessor
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_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 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_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 spectra
peakPantheR_start_GUI | peakPantheR Graphical User Interface
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
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

## -- R --

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')
retentionTimeCorrection | Apply retention time correction methods to adjust the retention time information in the uROI of peakPantheRAnnotation object
retentionTimeCorrection-method | Apply retention time correction methods to adjust the retention time information in the uROI of peakPantheRAnnotation object
ROI | ROI accessor returns targetFeatTable with cpdID, cpdName added
ROI-method | ROI accessor returns targetFeatTable with cpdID, cpdName added

## -- S --

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
spectraMetadata | spectraMetadata accessor
spectraMetadata-method | spectraMetadata accessor
spectraPaths_and_metadata_UI_helper | UI data import helper - prepare file paths and metadata
spectra_metadata_colourScheme_UI_helper | UI export plot helper - sample colour

## -- T --

TIC | TIC accessor
TIC-method | TIC accessor

## -- U --

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

## -- misc --

[-method | extract parts of peakPantheRAnnotation class