Package index
Data Processing Engines
R6 classes are used as processing engines for reading, processing, inspecting and storing data.
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CoreEngine - CoreEngine R6 class and methods
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MassSpecEngine - MassSpecEngine R6 class and methods
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RamanEngine - RamanEngine R6 class and methods
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StatisticEngine - StatisticEngine R6 class and methods
Processing settings
A data processing workflow in StreamFind is assemble by creating an ordered list of proessing settings objects. Each processing method is assigened to a processing engine and an algorithm.
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MassSpecSettings_AnnotateFeatures_StreamFind() - MassSpecSettings_AnnotateFeatures_StreamFind
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MassSpecSettings_AverageSpectra_StreamFind() - MassSpecSettings_AverageSpectra_StreamFind
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MassSpecSettings_BinSpectra_StreamFind() - MassSpecSettings_BinSpectra_StreamFind
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MassSpecSettings_CalculateFeaturesQuality_StreamFind() - MassSpecSettings_CalculateFeaturesQuality_StreamFind
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MassSpecSettings_CalculateSpectraCharges_StreamFind() - MassSpecSettings_CalculateSpectraCharges_StreamFind
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MassSpecSettings_ClusterSpectra_StreamFind() - MassSpecSettings_ClusterSpectra_StreamFind
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MassSpecSettings_CorrectChromatogramsBaseline_airpls() - MassSpecSettings_CorrectChromatogramsBaseline_airpls
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MassSpecSettings_CorrectChromatogramsBaseline_baseline_als() - MassSpecSettings_CorrectChromatogramsBaseline_baseline_als
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MassSpecSettings_CorrectMatrixSuppression_TiChri() - MassSpecSettings_CorrectMatrixSuppression_TiChri
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MassSpecSettings_CorrectSpectraBaseline_airpls() - MassSpecSettings_CorrectSpectraBaseline_airpls
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MassSpecSettings_CorrectSpectraBaseline_baseline_als() - MassSpecSettings_CorrectSpectraBaseline_baseline_als
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MassSpecSettings_DeconvoluteSpectra_StreamFind() - MassSpecSettings_DeconvoluteSpectra_StreamFind
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MassSpecSettings_FillFeatures_StreamFind() - MassSpecSettings_FillFeatures_StreamFind
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MassSpecSettings_FilterFeatures_patRoon() - MassSpecSettings_FilterFeatures_patRoon
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MassSpecSettings_FilterFeatures_StreamFind() - MassSpecSettings_FilterFeatures_StreamFind
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MassSpecSettings_FindFeatures_kpic2() - MassSpecSettings_FindFeatures_kpic2
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MassSpecSettings_FindFeatures_openms() - MassSpecSettings_FindFeatures_openms
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MassSpecSettings_FindFeatures_xcms3_centwave() - MassSpecSettings_FindFeatures_xcms3_centwave
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MassSpecSettings_FindFeatures_xcms3_matchedfilter() - MassSpecSettings_FindFeatures_xcms3_matchedfilter
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MassSpecSettings_FindInternalStandards_StreamFind() - MassSpecSettings_FindInternalStandards_StreamFind
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MassSpecSettings_FindSpectraMaxima_StreamFind() - MassSpecSettings_FindSpectraMaxima_StreamFind
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MassSpecSettings_GenerateCompounds_metfrag() - MassSpecSettings_GenerateCompounds_metfrag
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MassSpecSettings_GenerateFormulas_genform() - MassSpecSettings_GenerateFormulas_genform
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MassSpecSettings_GroupFeatures_openms() - MassSpecSettings_GroupFeatures_openms
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MassSpecSettings_GroupFeatures_xcms3_peakdensity() - MassSpecSettings_GroupFeatures_xcms3_peakdensity
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MassSpecSettings_GroupFeatures_xcms3_peakdensity_peakgroups() - MassSpecSettings_GroupFeatures_xcms3_peakdensity_peakgroups
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MassSpecSettings_IntegrateChromatograms_StreamFind() - MassSpecSettings_IntegrateChromatograms_StreamFind
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MassSpecSettings_IntegrateSpectra_StreamFind() - MassSpecSettings_IntegrateSpectra_StreamFind
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MassSpecSettings_LoadChromatograms_StreamFind() - MassSpecSettings_LoadChromatograms_StreamFind
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MassSpecSettings_LoadFeaturesEIC_StreamFind() - MassSpecSettings_LoadFeaturesEIC_StreamFind
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MassSpecSettings_LoadFeaturesMS1_StreamFind() - MassSpecSettings_LoadFeaturesMS1_StreamFind
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MassSpecSettings_LoadFeaturesMS2_StreamFind() - MassSpecSettings_LoadFeaturesMS2_StreamFind
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MassSpecSettings_LoadMSPeakLists_patRoon() - MassSpecSettings_LoadMSPeakLists_patRoon
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MassSpecSettings_LoadMSPeakLists_StreamFind() - MassSpecSettings_LoadMSPeakLists_StreamFind
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MassSpecSettings_LoadSpectra_StreamFind() - MassSpecSettings_LoadSpectra_StreamFind
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MassSpecSettings_NormalizeSpectra_blockweight() - MassSpecSettings_NormalizeSpectra_blockweight
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MassSpecSettings_NormalizeSpectra_meancenter() - MassSpecSettings_NormalizeSpectra_meancenter
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MassSpecSettings_NormalizeSpectra_minmax() - MassSpecSettings_NormalizeSpectra_minmax
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MassSpecSettings_NormalizeSpectra_scale() - MassSpecSettings_NormalizeSpectra_scale
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MassSpecSettings_NormalizeSpectra_snv() - MassSpecSettings_NormalizeSpectra_snv
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MassSpecSettings_QuantifyChromatographicPeaks_StreamFind() - MassSpecSettings_QuantifyChromatographicPeaks_StreamFind
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MassSpecSettings_SmoothChromatograms_movingaverage() - MassSpecSettings_SmoothChromatograms_movingaverage
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MassSpecSettings_SmoothChromatograms_savgol() - MassSpecSettings_SmoothChromatograms_savgol
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MassSpecSettings_SmoothSpectra_movingaverage() - MassSpecSettings_SmoothSpectra_movingaverage
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MassSpecSettings_SmoothSpectra_savgol() - MassSpecSettings_SmoothSpectra_savgol
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MassSpecSettings_SubtractBlankSpectra_StreamFind() - MassSpecSettings_SubtractBlankSpectra_StreamFind
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MassSpecSettings_SuspectScreening_forident() - MassSpecSettings_SuspectScreening_forident
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MassSpecSettings_SuspectScreening_patRoon() - MassSpecSettings_SuspectScreening_patRoon
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MassSpecSettings_SuspectScreening_StreamFind() - MassSpecSettings_SuspectScreening_StreamFind
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RamanSettings_AverageSpectra_StreamFind() - RamanSettings_AverageSpectra_StreamFind
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RamanSettings_BinSpectra_StreamFind() - RamanSettings_BinSpectra_StreamFind
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RamanSettings_CorrectSpectraBaseline_airpls() - RamanSettings_CorrectSpectraBaseline_airpls
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RamanSettings_CorrectSpectraBaseline_baseline_als() - RamanSettings_CorrectSpectraBaseline_baseline_als
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RamanSettings_DeleteSpectraSection_StreamFind() - RamanSettings_DeleteSpectraSection_StreamFind
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RamanSettings_MergeSpectraTimeSeries_StreamFind() - RamanSettings_MergeSpectraTimeSeries_StreamFind
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RamanSettings_NormalizeSpectra_blockweight() - RamanSettings_NormalizeSpectra_blockweight
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RamanSettings_NormalizeSpectra_meancenter() - RamanSettings_NormalizeSpectra_meancenter
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RamanSettings_NormalizeSpectra_minmax() - RamanSettings_NormalizeSpectra_minmax
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RamanSettings_NormalizeSpectra_scale() - RamanSettings_NormalizeSpectra_scale
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RamanSettings_NormalizeSpectra_snv() - RamanSettings_NormalizeSpectra_snv
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RamanSettings_SmoothSpectra_movingaverage() - RamanSettings_SmoothSpectra_movingaverage
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RamanSettings_SmoothSpectra_savgol() - RamanSettings_SmoothSpectra_savgol
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RamanSettings_SubtractBlankSpectra_StreamFind() - RamanSettings_SubtractBlankSpectra_StreamFind
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RamanSettings_SubtractSpectraSection_StreamFind() - RamanSettings_SubtractSpectraSection_StreamFind
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StatisticSettings_MakeModel_knn() - StatisticSettings_MakeModel_knn
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StatisticSettings_MakeModel_mcrals_mdatools() - StatisticSettings_MakeModel_mcrals_mdatools
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StatisticSettings_MakeModel_mcrpure_mdatools() - StatisticSettings_MakeModel_mcrpure_mdatools
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StatisticSettings_MakeModel_pca_mdatools() - StatisticSettings_MakeModel_pca_mdatools
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StatisticSettings_PrepareData_autoscale() - StatisticSettings_PrepareData_autoscale
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StatisticSettings_Quantify_mcrals() - StatisticSettings_Quantify_mcrals
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convert_ms_files() - Function to convert vendor MS files to mzML or mzXML
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trim_ms_files_spectra() - Function to trim spectra in mzML or mzXML files
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clear_cache() - clear_cache
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run_app() - Run the Shiny Application