phenomecentre/peakPantheR
Peak Picking and Annotation of High Resolution Experiments

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244
Source code
88
Man pages
75
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phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments
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API

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

Global functions
.onAttach Source code
.onLoad Source code
EICs Man page
EICs,peakPantheRAnnotation-method Man page
FIR Man page
FIR,peakPantheRAnnotation-method Man page
ROI Man page
ROI,peakPantheRAnnotation-method Man page
ROIStatistics_calculateMeanISRT Source code
ROIStatistics_check_ROI_meanIS Source code
ROIStatistics_init_checks Source code
ROIStatistics_saveEICsROI Source code
TIC Man page
TIC,peakPantheRAnnotation-method Man page
[,peakPantheRAnnotation,ANY,ANY,ANY-method Man page
[,peakPantheRAnnotation-method Man page
acquisitionTime Man page
acquisitionTime,peakPantheRAnnotation-method Man page
annotDiagMultiplot_generateMulti Source code
annotDiagMultiplot_initPlot Source code
annotDiagMultiplot_linkAxes Source code
annotDiagMultiplot_singleCpd Source code
annotationDiagnosticMultiplot Man page Source code
annotationDiagnosticPlots Man page
annotationDiagnosticPlots,peakPantheRAnnotation-method Man page
annotationParamsDiagnostic Man page
annotationParamsDiagnostic,peakPantheRAnnotation-method Man page
annotationParamsDiagnostic_FIR Source code
annotationParamsDiagnostic_uROI Source code
annotationTable Man page
annotationTable,peakPantheRAnnotation-method Man page
annotation_diagnostic_multiplot_UI_helper Man page Source code
annotation_fit_summary_UI_helper Man page Source code
annotation_showMethod_UI_helper Man page Source code
annotation_showText_UI_helper Man page Source code
applyRTCorrection_checkInput Source code
applyRTCorrection_checkInputParams Source code
applyRTCorrection_checkInput_checkReferenceTable Source code
applyRTCorrection_checkTargetFeatTable Source code
applyRTCorrection_correctFeatTable Source code
check_NA_in_target_parameters Source code
cpdID Man page
cpdID,peakPantheRAnnotation-method Man page
cpdMetadata Man page
cpdMetadata,peakPantheRAnnotation-method Man page
cpdName Man page
cpdName,peakPantheRAnnotation-method Man page
dataPoints Man page
dataPoints,peakPantheRAnnotation-method Man page
dynamic_max_trials Source code
emgGaussian_guess Man page Source code
emgGaussian_minpack.lm Man page Source code
emgGaussian_minpack.lm_objectiveFun Man page Source code
extractSignalRawData Man page Source code
extractSignalRawData_checkInput Source code
extractSignalRawData_extractFromWindows Source code
extractSignalRawData_extractScans Source code
extractSignalRawData_init Source code
filename Man page
filename,peakPantheRAnnotation-method Man page
filepath Man page
filepath,peakPantheRAnnotation-method Man page
findTargetFeatures Man page Source code
findTargetFeatures_checkInput Source code
findTargetFeatures_findMZ Source code
findTargetFeatures_findRTMinMax Source code
findTargetFeatures_findRTproperties Source code
findTargetFeatures_fitFeature Source code
findTargetFeatures_fitQuality Source code
findTargetFeatures_fitcurve Source code
findTargetFeatures_initOutput Source code
findTargetFeatures_integCurve Source code
fitCurve Man page Source code
fitCurve_emgGaussian Source code
fitCurve_skewedGaussian Source code
fit_RANSAC Source code
fit_RANSAC_checkFinalConvergence Source code
fit_RANSAC_checkInput Source code
fit_RANSAC_coreOptimization Source code
fit_polynomial Source code
gaussian_cerf Man page Source code
gaussian_erf Man page Source code
generateIonChromatogram Man page Source code
getAcquisitionDatemzML Man page Source code
getTargetFeatureStatistic Man page Source code
initialise_annotation_from_files_UI_helper Man page Source code
initialize_checkTargetFeatTable Source code
initialize_spectraPaths Source code
initialize_targetFeatTable Source code
integrateFIR Man page Source code
integrateFIR_features Source code
is.peakPantheR_curveFit Man page Source code
isAnnotated Man page
isAnnotated,peakPantheRAnnotation-method Man page
load_annotation_from_file_UI_helper Man page Source code
loss_absolute Source code
loss_squared Source code
nbCompounds Man page
nbCompounds,peakPantheRAnnotation-method Man page
nbSamples Man page
nbSamples,peakPantheRAnnotation-method Man page
outputAnnotationDiagnostic Man page
outputAnnotationDiagnostic,peakPantheRAnnotation-method Man page
outputAnnotationDiagnostic_saveSingleMultiPlot Source code
outputAnnotationFeatureMetadata_UI_helper Man page Source code
outputAnnotationParamsCSV Man page
outputAnnotationParamsCSV,peakPantheRAnnotation-method Man page
outputAnnotationResult Man page
outputAnnotationResult,peakPantheRAnnotation-method Man page
outputAnnotationResult_saveCpdMetadata Source code
outputAnnotationResult_savePeaktable Source code
outputAnnotationResult_saveSpectraMetadata Source code
outputAnnotationResult_saveSummary Source code
outputAnnotationSpectraMetadata_UI_helper Man page Source code
parallelAnnotation_init Source code
parallelAnnotation_parallelHelper Source code
parallelAnnotation_process Source code
parallelAnnotation_runSingleFileSearch Source code
peakFit Man page
peakFit,peakPantheRAnnotation-method Man page
peakPantheR Man page
peakPantheR-package Man page
peakPantheRAnnotation Man page Source code
peakPantheRAnnotation-class Man page
peakPantheR_ROIStatistics Man page Source code
peakPantheR_applyRTCorrection Man page Source code
peakPantheR_loadAnnotationParamsCSV Man page Source code
peakPantheR_parallelAnnotation Man page Source code
peakPantheR_plotEICFit Man page Source code
peakPantheR_plotPeakwidth Man page Source code
peakPantheR_quickEIC Man page Source code
peakPantheR_singleFileSearch Man page Source code
peakPantheR_start_GUI Man page Source code
peakTables Man page
peakTables,peakPantheRAnnotation-method Man page
peak_shape_stat Source code
plotEICDetectedPeakwidth Man page Source code
plotEICDetectedPeakwidth_checkInp Source code
plotEICFit_checkInput Source code
plotEICFit_prepData Source code
plotHistogram Man page Source code
plotPeakwidth_checkInput Source code
plotPeakwidth_plotWidthApex Source code
plotPeakwidth_rotateAxis_setLabels Source code
predictCurve Man page Source code
prepare_advanced_target_parameters Man page Source code
prepare_basic_target_parameters Man page Source code
resetAnnot_newTargetFeatTable Source code
resetAnnot_prevTargetFeatTable Source code
resetAnnot_spectraPathMetadata Source code
resetAnnot_targetFeatTable_uROI_FIR_cpdMeta Source code
resetAnnot_uROIExist Source code
resetAnnot_useUROIuseFIR Source code
resetAnnotation Man page
resetAnnotation,peakPantheRAnnotation-method Man page
resetFIR Man page
resetFIR,peakPantheRAnnotation-method Man page
retentionTimeCorrection Man page
retentionTimeCorrection,peakPantheRAnnotation-method Man page
retry Source code
rtCorrection_checkInput Source code
rtCorrection_diagnosticPlot Source code
rtCorrection_prepareAnnotation Source code
rtCorrection_prepareTargetFeatTable Source code
saveSingleFileMultiEIC Man page Source code
singleDiagnosticPlots Source code
singleFileSearch_checkInput Source code
singleFileSearch_integrate Source code
skewedGaussian_guess Man page Source code
skewedGaussian_minpack.lm Man page Source code
skewedGaussian_minpack.lm_objectiveFun Man page Source code
spectraMetadata Man page
spectraMetadata,peakPantheRAnnotation-method Man page
spectraPaths_and_metadata_UI_helper Man page Source code
spectra_metadata_colourScheme_UI_helper Man page Source code
subset_annot_diag_plot_UI_helper Source code
subsetting_peakTables_dataPoints_peakFit Source code
uROI Man page
uROI,peakPantheRAnnotation-method Man page
uROIExist Man page
uROIExist,peakPantheRAnnotation-method Man page
useFIR Man page
useFIR,peakPantheRAnnotation-method Man page
useUROI Man page
useUROI,peakPantheRAnnotation-method Man page
valid_peakPantheRAnnotation Source code
valid_ppR_FIR Source code
valid_ppR_ROI Source code
valid_ppR_ROI_content Source code
valid_ppR_TIC Source code
valid_ppR_acquisitionTime Source code
valid_ppR_cpdMetadata Source code
valid_ppR_cpdName Source code
valid_ppR_dataPoints Source code
valid_ppR_dataPoints_content Source code
valid_ppR_peakFit Source code
valid_ppR_peakTables Source code
valid_ppR_spectraMetadata Source code
valid_ppR_uROI Source code
valid_ppR_uROI_content Source code
valid_ppR_useUROIuROIExist Source code
phenomecentre/peakPantheR documentation built on Feb. 29, 2024, 9:07 p.m.

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