Package: peakPantheR 1.21.0

Arnaud Wolfer

peakPantheR: Peak Picking and Annotation of High Resolution Experiments

An automated pipeline for the detection, integration and reporting of predefined features across a large number of mass spectrometry data files. It enables the real time annotation of multiple compounds in a single file, or the parallel annotation of multiple compounds in multiple files. A graphical user interface as well as command line functions will assist in assessing the quality of annotation and update fitting parameters until a satisfactory result is obtained.

Authors:Arnaud Wolfer [aut, cre], Goncalo Correia [aut], Jake Pearce [ctb], Caroline Sands [ctb]

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peakPantheR.pdf |peakPantheR.html✨
peakPantheR/json (API)
NEWS

# Install 'peakPantheR' in R:
install.packages('peakPantheR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/phenomecentre/peakpanther/issues

On BioConductor:peakPantheR-1.21.0(bioc 3.21)peakPantheR-1.20.0(bioc 3.20)

massspectrometrymetabolomicspeakdetectionfeature-detectionmass-spectrometry

6.82 score 12 stars 23 scripts 172 downloads 49 exports 141 dependencies

Last updated 2 months agofrom:4d6e9772c5. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-winOKNov 27 2024
R-4.5-linuxOKNov 27 2024
R-4.4-winOKNov 27 2024
R-4.4-macERRORNov 27 2024
R-4.3-winOKNov 27 2024
R-4.3-macERRORNov 27 2024

Exports:acquisitionTimeannotation_diagnostic_multiplot_UI_helperannotation_fit_summary_UI_helperannotation_showMethod_UI_helperannotation_showText_UI_helperannotationDiagnosticPlotsannotationParamsDiagnosticannotationTablecpdIDcpdMetadatacpdNamedataPointsEICsfilenamefilepathFIRinitialise_annotation_from_files_UI_helperisAnnotatedload_annotation_from_file_UI_helpernbCompoundsnbSamplesoutputAnnotationDiagnosticoutputAnnotationFeatureMetadata_UI_helperoutputAnnotationParamsCSVoutputAnnotationResultoutputAnnotationSpectraMetadata_UI_helperpeakFitpeakPantheR_loadAnnotationParamsCSVpeakPantheR_parallelAnnotationpeakPantheR_plotEICFitpeakPantheR_plotPeakwidthpeakPantheR_quickEICpeakPantheR_ROIStatisticspeakPantheR_singleFileSearchpeakPantheR_start_GUIpeakPantheRAnnotationpeakTablesresetAnnotationresetFIRretentionTimeCorrectionROIspectra_metadata_colourScheme_UI_helperspectraMetadataspectraPaths_and_metadata_UI_helperTICuROIuROIExistuseFIRuseUROI

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbslibcachemcliclueclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrDTevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalubridatemagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminpack.lmMsCoreUtilsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpracmapreprocessCorepromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRColorBrewerRcppreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalesshinyshinycssloaderssnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsvglitesyssystemfontstibbletidyrtidyselecttimechangetinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxfunXMLxtableXVectoryamlzlibbioc

Getting Started with the peakPantheR package

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2023-10-02
Started: 2018-02-26

Parallel Annotation

Rendered fromparallel-annotation.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2023-10-02
Started: 2018-02-26

peakPantheR Graphical User Interface

Arnaud Wolfer

Rendered frompeakPantheR-GUI.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2021-12-20
Started: 2020-10-13

Real Time Annotation

Rendered fromreal-time-annotation.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2023-10-02
Started: 2018-02-26

Readme and manuals

Help Manual

Help pageTopics
extract parts of peakPantheRAnnotation class[,peakPantheRAnnotation,ANY,ANY,ANY-method [,peakPantheRAnnotation-method
acquisitionTime accessor returns value as.POSIXctacquisitionTime acquisitionTime,peakPantheRAnnotation-method
UI diagnostic plot helper - single feature multiplotannotation_diagnostic_multiplot_UI_helper
UI diagnostic table - fit summaryannotation_fit_summary_UI_helper
UI show annotation helper - list of propertiesannotation_showMethod_UI_helper
UI show annotation helper - UI sidebar stringannotation_showText_UI_helper
Generate a multiplot of all diagnostic plotsannotationDiagnosticMultiplot
Generate fit diagnostic plotsannotationDiagnosticPlots annotationDiagnosticPlots,peakPantheRAnnotation-method
Set uROI and FIR based on annotation resultsannotationParamsDiagnostic annotationParamsDiagnostic,peakPantheRAnnotation-method
annotationTable accessorannotationTable annotationTable,peakPantheRAnnotation-method
cpdID accessorcpdID cpdID,peakPantheRAnnotation-method
cpdMetadata accessorcpdMetadata cpdMetadata,peakPantheRAnnotation-method
cpdName accessorcpdName cpdName,peakPantheRAnnotation-method
dataPoints accessordataPoints dataPoints,peakPantheRAnnotation-method
EICs accessorEICs EICs,peakPantheRAnnotation-method
Guess function for initial exponentially modified gaussian parameters and boundsemgGaussian_guess
Implementation of the Exponentially Modified Gaussian (EMG) peak shape for use with minpack.lmemgGaussian_minpack.lm
Exponentially Modified Gaussian minpack.lm objective functionemgGaussian_minpack.lm_objectiveFun
Extract signal in a multiple defined mz rt window from a raw data fileextractSignalRawData
filename accessor by spliting filepathfilename filename,peakPantheRAnnotation-method
filepath accessorfilepath filepath,peakPantheRAnnotation-method
Find and integrate target features in each ROIfindTargetFeatures
FIR accessor returns targetFeatTable with cpdID, cpdName addedFIR FIR,peakPantheRAnnotation-method
Curve fitting using minpack.lmfitCurve
Gaussian Error functiongaussian_cerf
Gaussian Error functiongaussian_erf
Generate ion chromatogram from raw data pointsgenerateIonChromatogram
Parse acquisition date from a mzML filegetAcquisitionDatemzML
Calculate chromatographic peak propertiesgetTargetFeatureStatistic
UI data import helper - initialise new annotation from filesinitialise_annotation_from_files_UI_helper
Integrate fallback integration regionsintegrateFIR
Check if object is of class peakPantheR_curveFitis.peakPantheR_curveFit
isAnnotated accessorisAnnotated isAnnotated,peakPantheRAnnotation-method
UI data import helper - check loaded annotationload_annotation_from_file_UI_helper
nbCompounds accessor established on cpdIDnbCompounds nbCompounds,peakPantheRAnnotation-method
nbSamples accessor established on filepathnbSamples nbSamples,peakPantheRAnnotation-method
Save to disk the annotation parameters as CSV and a diagnostic plot per fitted compoundoutputAnnotationDiagnostic outputAnnotationDiagnostic,peakPantheRAnnotation-method
UI export helper - feature metadataoutputAnnotationFeatureMetadata_UI_helper
Save annotation parameters as CSVoutputAnnotationParamsCSV outputAnnotationParamsCSV,peakPantheRAnnotation-method
Save to disk all annotation results as csv filesoutputAnnotationResult outputAnnotationResult,peakPantheRAnnotation-method
UI export helper - spectra path and metadataoutputAnnotationSpectraMetadata_UI_helper
peakFit accessorpeakFit peakFit,peakPantheRAnnotation-method
peakPantheR: A package for Peak Picking and ANnoTation of High resolution ExperimentspeakPantheR-package peakPantheR
Correct targeted retention time based on reference compoundspeakPantheR_applyRTCorrection
Load fit parameters from CSVpeakPantheR_loadAnnotationParamsCSV
Search, integrate and report targeted features in a multiple spectrapeakPantheR_parallelAnnotation
Plot samples raw data and detected feature for a single ROIpeakPantheR_plotEICFit
Plot peak value and peakwidth by acquisition time or in input orderpeakPantheR_plotPeakwidth
Extract and plot a EIC from a raw data filepeakPantheR_quickEIC
Save to disk each ROI EIC and mean IS RTpeakPantheR_ROIStatistics
Search, integrate and report targeted features in a raw spectrapeakPantheR_singleFileSearch
peakPantheR Graphical User InterfacepeakPantheR_start_GUI
An S4 class to represent peakPantheR annotation resultspeakPantheRAnnotation peakPantheRAnnotation-class
peakTables accessor with cpdID and cpdName added backpeakTables peakTables,peakPantheRAnnotation-method
Plot samples raw data and detected feature for a single ROIplotEICDetectedPeakwidth
Plot variable histogram and densityplotHistogram
Predict curve valuespredictCurve
Process target region parameters (with uROI, FIR) for object initialisationprepare_advanced_target_parameters
Process target region parameters (simple format) for object initialisationprepare_basic_target_parameters
Reset a peakPantheRAnnotation and alter samples and compounds informationresetAnnotation resetAnnotation,peakPantheRAnnotation-method
Reset FIR windows to uROI or ROI values Reset FIR windows to uROI (or ROI if 'uROIExist=FALSE')resetFIR resetFIR,peakPantheRAnnotation-method
Apply retention time correction methods to adjust the retention time information in the uROI of peakPantheRAnnotation objectretentionTimeCorrection retentionTimeCorrection,peakPantheRAnnotation-method
ROI accessor returns targetFeatTable with cpdID, cpdName addedROI ROI,peakPantheRAnnotation-method
Save to disk a plot of all ROI EIC and detected feature rangesaveSingleFileMultiEIC
Guess function for initial skewed gaussian parameters and boundsskewedGaussian_guess
Implementation of the Skewed Gaussian peak shape for use with minpack.lmskewedGaussian_minpack.lm
Skewed Gaussian minpack.lm objective functionskewedGaussian_minpack.lm_objectiveFun
UI export plot helper - sample colourspectra_metadata_colourScheme_UI_helper
spectraMetadata accessorspectraMetadata spectraMetadata,peakPantheRAnnotation-method
UI data import helper - prepare file paths and metadataspectraPaths_and_metadata_UI_helper
TIC accessorTIC TIC,peakPantheRAnnotation-method
uROI accessor returns targetFeatTable with cpdID, cpdName addeduROI uROI,peakPantheRAnnotation-method
uROIExist accessoruROIExist uROIExist,peakPantheRAnnotation-method
useFIR accessoruseFIR useFIR,peakPantheRAnnotation-method
useUROI accessoruseUROI useUROI,peakPantheRAnnotation-method