Package index

Introduction

StreamFind is built with two main class systems: R6 and S3. The R6 system is used for data processing engine classes, which are used for project managing. The S3 system is used for classes to manage metadata, analyses, data processing, results, audit trail and configuration. Below all class constructors and methods exposed to the user are listed.

Engines (R6)

Engine: Generic (top level) Engine class for project management

MassSpecEngine: Engine dedicated to Mass Spectrometry (MS) data processing

RamanEngine: Engine dedicated to Raman spectroscopic data processing

StatisticEngine: Engine dedicated to statistical analysis

Metadata (S3)

Metadata classes are used to manage metadata (e.g., date, author and description) of main classes, such as the R6 engine classes.

Metadata() validate_object(<Metadata>) length(<Metadata>) names(<Metadata>) `[`(<Metadata>) `[<-`(<Metadata>) `[[`(<Metadata>) `[[<-`(<Metadata>) save(<Metadata>) read(<Metadata>) show(<Metadata>): Generic (top level) Metadata constructor and methods

Analyses (S3)

Analyses represent data (i.e., actual data or links to raw data files) and results. Analyses child classes are implemented for each type of data.

Analyses() validate_object(<Analyses>): Generic (top level ) Analyses class and methods

Data Processing (S3)

Data processing is governed by the Workflow class which consists of a sequence of ProcessingStep class objects. Processing methods for a specific type of data are implemented as child classes of the ProcessingStep class.

Workflow() validate_object(<Workflow>) info(<Workflow>) get_methods(<Workflow>) `[`(<Workflow>) `[<-`(<Workflow>) `[[`(<Workflow>) `[[<-`(<Workflow>) save(<Workflow>) read(<Workflow>) show(<Workflow>): Generic (top level) Workflow class and methods

ProcessingStep() validate_object(<ProcessingStep>) as.ProcessingStep() save(<ProcessingStep>) read(<ProcessingStep>) show(<ProcessingStep>): Generic (top level) ProcessingStep class and methods

Mass Spectrometry Methods

MassSpecMethod_AnnotateFeatures_StreamFind(): Mass Spectrometry Method for Annotating Features in MassSpecResults_NonTargetAnalysis (StreamFind algorithm)

MassSpecMethod_AverageSpectra_StreamFind(): MassSpecMethod_AverageSpectra_StreamFind Class

MassSpecMethod_BinSpectra_StreamFind(): MassSpecMethod_BinSpectra_StreamFind Class

MassSpecMethod_CalculateFeaturesQuality_StreamFind(): Mass Spectrometry Method to Calculate Features Quality (StreamFind algorithm)

MassSpecMethod_CalculateSpectraCharges_native(): MassSpecMethod_CalculateSpectraCharges_native Class

MassSpecMethod_ClusterSpectra_StreamFind(): MassSpecMethod_ClusterSpectra_StreamFind Class

MassSpecMethod_CorrectChromatogramsBaseline_airpls(): MassSpecMethod_CorrectChromatogramsBaseline_airpls Class

MassSpecMethod_CorrectChromatogramsBaseline_baseline_als(): MassSpecMethod_CorrectChromatogramsBaseline_baseline_als Class

MassSpecMethod_CorrectMatrixSuppression_TiChri(): MassSpecMethod_CorrectMatrixSuppression_TiChri Class

MassSpecMethod_CorrectSpectraBaseline_airpls(): MassSpecMethod_CorrectSpectraBaseline_airpls Class

MassSpecMethod_CorrectSpectraBaseline_baseline_als(): MassSpecMethod_CorrectSpectraBaseline_baseline_als Class

MassSpecMethod_DeconvoluteSpectra_native(): MassSpecMethod_DeconvoluteSpectra_native Class

MassSpecMethod_FillFeatures_StreamFind(): MassSpecMethod_FillFeatures_StreamFind Class

MassSpecMethod_FilterChromPeaks_native(): MassSpecMethod_FilterChromPeaks_native Class

MassSpecMethod_FilterFeaturesMS2_native(): MassSpecMethod_FilterFeaturesMS2_native Class

MassSpecMethod_FilterFeatures_patRoon(): MassSpecMethod_FilterFeatures_patRoon Class

MassSpecMethod_FilterFeatures_StreamFind(): MassSpecMethod_FilterFeatures_StreamFind Class

MassSpecMethod_FindChromPeaks_LocalMaxima(): MassSpecMethod_FindChromPeaks_LocalMaxima Class

MassSpecMethod_FindChromPeaks_pracma(): MassSpecMethod_FindChromPeaks_pracma Class

MassSpecMethod_FindFeatures_kpic2(): MassSpecMethod_FindFeatures_kpic2 class

MassSpecMethod_FindFeatures_openms(): MassSpecMethod_FindFeatures_openms class

MassSpecMethod_FindFeatures_qalgorithms(): MassSpecMethod_FindFeatures_qalgorithms class

MassSpecMethod_FindFeatures_xcms3_centwave(): MassSpecMethod_FindFeatures_xcms3_centwave class

MassSpecMethod_FindFeatures_xcms3_matchedfilter(): MassSpecMethod_FindFeatures_xcms3_matchedfilter class

MassSpecMethod_FindInternalStandards_StreamFind(): MassSpecMethod_FindInternalStandards_StreamFind Class

MassSpecMethod_FindSpectraMaxima_native(): MassSpecMethod_FindSpectraMaxima_native Class

MassSpecMethod_GenerateCompounds_metfrag(): MassSpecMethod_GenerateCompounds_metfrag Class

MassSpecMethod_GenerateFormulas_genform(): MassSpecMethod_GenerateFormulas_genform Class

MassSpecMethod_GroupFeatures_openms(): MassSpecMethod_GroupFeatures_openms Class

MassSpecMethod_GroupFeatures_xcms3_peakdensity(): MassSpecMethod_GroupFeatures_xcms3_peakdensity Class

MassSpecMethod_GroupFeatures_xcms3_peakdensity_peakgroups(): MassSpecMethod_GroupFeatures_xcms3_peakdensity_peakgroups Class

MassSpecMethod_IntegrateChromatograms_pracma(): MassSpecMethod_IntegrateChromatograms_pracma Class

MassSpecMethod_IntegrateSpectra_StreamFind(): MassSpecMethod_IntegrateSpectra_StreamFind Class

MassSpecMethod_LoadChromatograms_native(): MassSpecMethod_LoadChromatograms_native Class

MassSpecMethod_LoadFeaturesEIC_StreamFind(): MassSpecMethod_LoadFeaturesEIC_StreamFind S3 Class

MassSpecMethod_LoadFeaturesMS1_StreamFind(): MassSpecMethod_LoadFeaturesMS1_StreamFind S3 Class

MassSpecMethod_LoadFeaturesMS2_StreamFind(): MassSpecMethod_LoadFeaturesMS2_StreamFind S3 Class

MassSpecMethod_LoadSpectra_chrompeaks(): MassSpecMethod_LoadSpectra_chrompeaks S3 Class

MassSpecMethod_LoadSpectra_native(): MassSpecMethod_LoadSpectra_native S3 Class

MassSpecMethod_NormalizeSpectra_blockweight(): MassSpecMethod_NormalizeSpectra_blockweight Class

MassSpecMethod_NormalizeSpectra_meancenter(): MassSpecMethod_NormalizeSpectra_meancenter Class

MassSpecMethod_NormalizeSpectra_minmax(): MassSpecMethod_NormalizeSpectra_minmax Class

MassSpecMethod_NormalizeSpectra_scale(): MassSpecMethod_NormalizeSpectra_scale Class

MassSpecMethod_NormalizeSpectra_snv(): MassSpecMethod_NormalizeSpectra_snv Class

MassSpecMethod_QuantifyChromatographicPeaks_native(): MassSpecMethod_QuantifyChromatographicPeaks_native Class

MassSpecMethod_SmoothChromatograms_movingaverage(): MassSpecMethod_SmoothChromatograms_movingaverage Class

MassSpecMethod_SmoothChromatograms_savgol(): MassSpecMethod_SmoothChromatograms_savgol Class

MassSpecMethod_SmoothSpectra_movingaverage(): MassSpecMethod_SmoothSpectra_movingaverage Class

MassSpecMethod_SmoothSpectra_savgol(): MassSpecMethod_SmoothSpectra_savgol Class

MassSpecMethod_SubtractBlankSpectra_StreamFind(): MassSpecMethod_SubtractBlankSpectra_StreamFind Class

MassSpecMethod_SuspectScreening_forident(): MassSpecMethod_SuspectScreening_forident Class

MassSpecMethod_SuspectScreening_patRoon(): MassSpecMethod_SuspectScreening_patRoon Class

MassSpecMethod_SuspectScreening_StreamFind(): MassSpecMethod_SuspectScreening_StreamFind Class

Raman Spectroscopy Methods

RamanMethod_AddShiftValues_native(): RamanMethod_AddShiftValues_native Class

RamanMethod_AverageSpectra_native(): Raman Method to Average Spectra (native algorithm)

RamanMethod_BinScans_native(): Raman Method for Binning Time Scans (native algorithm)

RamanMethod_BinSpectra_StreamFind(): RamanMethod_BinSpectra_StreamFind Class

RamanMethod_CalculateSpectraSimilary_hqi(): RamanMethod_CalculateSpectraSimilary_hqi Class

RamanMethod_CorrectSpectraBaseline_airpls(): RamanMethod_CorrectSpectraBaseline_airpls Class

RamanMethod_CorrectSpectraBaseline_baseline_als(): RamanMethod_CorrectSpectraBaseline_baseline_als Class

RamanMethod_DeleteScansSection_native(): RamanMethod_DeleteScansSection_native Class

RamanMethod_DeleteSpectraSection_native(): RamanMethod_DeleteSpectraSection_native Class

RamanMethod_FilterChromPeaks_native(): RamanMethod_FilterChromPeaks_native Class

RamanMethod_FilterSpectra_native(): RamanMethod_FilterSpectra_native Class

RamanMethod_FindChromPeaks_LocalMaxima(): RamanMethod_FindChromPeaks_LocalMaxima Class

RamanMethod_FindChromPeaks_pracma(): RamanMethod_FindChromPeaks_pracma Class

RamanMethod_GroupPeaks_native(): RamanMethod_GroupPeaks_native Class

RamanMethod_InvertAxis_intensity(): RamanMethod_InvertAxis_intensity Class

RamanMethod_MergeSpectraTimeSeries_StreamFind(): RamanMethod_MergeSpectraTimeSeries_StreamFind

RamanMethod_NormalizeSpectra_blockweight(): RamanMethod_NormalizeSpectra_blockweight Class

RamanMethod_NormalizeSpectra_meancenter(): RamanMethod_NormalizeSpectra_meancenter Class

RamanMethod_NormalizeSpectra_minmax(): RamanMethod_NormalizeSpectra_minmax Class

RamanMethod_NormalizeSpectra_scale(): RamanMethod_NormalizeSpectra_scale Class

RamanMethod_NormalizeSpectra_snv(): RamanMethod_NormalizeSpectra_snv Class

RamanMethod_RemoveCosmicRays_native(): RamanMethod_RemoveCosmicRays_native

RamanMethod_ScaleTime_native(): RamanMethod_ScaleTime_native Class

RamanMethod_SmoothSpectra_movingaverage(): RamanMethod_SmoothSpectra_movingaverage

RamanMethod_SmoothSpectra_savgol(): RamanMethod_SmoothSpectra_savgol Class

RamanMethod_SubtractBlankSpectra_StreamFind(): RamanMethod_SubtractBlankSpectra_StreamFind Class

RamanMethod_SubtractScansSection_native(): RamanMethod_SubtractScansSection_native Class

RamanMethod_SubtractSpectraSection_StreamFind(): RamanMethod_SubtractSpectraSection_StreamFind Class

Statistic Methods

StatisticMethod_MakeModel_knn_class(): StatisticMethod_MakeModel_knn_class Class

StatisticMethod_MakeModel_mcrals_mdatools(): StatisticMethod_MakeModel_mcrals_mdatools Class

StatisticMethod_MakeModel_mcrpure_mdatools(): StatisticMethod_MakeModel_mcrpure_mdatools Class

StatisticMethod_MakeModel_pca_mdatools(): StatisticMethod_MakeModel_pca_mdatools Class

Results (S3)

The Results classes represent results of specific data processing methods. Results child classes are implemented for each processing method but can be reused/updated across processing methods. For instance, normalizing averaged spectra will update the spectra results.

Results() validate_object(<Results>): Generic (top level) Results class constructor and methods

Mass Spectrometry Results

MassSpecResults_Chromatograms() validate_object(<MassSpecResults_Chromatograms>) show(<MassSpecResults_Chromatograms>) `[`(<MassSpecResults_Chromatograms>) get_chromatograms(<MassSpecResults_Chromatograms>) plot_chromatograms(<MassSpecResults_Chromatograms>) plot_chromatograms_baseline(<MassSpecResults_Chromatograms>) get_chromatograms_peaks(<MassSpecResults_Chromatograms>) plot_chromatograms_peaks(<MassSpecResults_Chromatograms>): Constructor and methods to handle Mass Spectrometry chromatograms results

MassSpecResults_NonTargetAnalysis() validate_object(<MassSpecResults_NonTargetAnalysis>) show(<MassSpecResults_NonTargetAnalysis>) as.MassSpecResults_NonTargetAnalysis() `[`(<MassSpecResults_NonTargetAnalysis>) `[[`(<MassSpecResults_NonTargetAnalysis>) get_features_count(<MassSpecResults_NonTargetAnalysis>) plot_features_count(<MassSpecResults_NonTargetAnalysis>) get_features(<MassSpecResults_NonTargetAnalysis>) map_features(<MassSpecResults_NonTargetAnalysis>) map_features_intensity(<MassSpecResults_NonTargetAnalysis>) get_features_eic(<MassSpecResults_NonTargetAnalysis>) plot_features(<MassSpecResults_NonTargetAnalysis>) get_features_ms1(<MassSpecResults_NonTargetAnalysis>) plot_features_ms1(<MassSpecResults_NonTargetAnalysis>) get_features_ms2(<MassSpecResults_NonTargetAnalysis>) plot_features_ms2(<MassSpecResults_NonTargetAnalysis>) get_groups(<MassSpecResults_NonTargetAnalysis>) plot_groups(<MassSpecResults_NonTargetAnalysis>) plot_groups_overview(<MassSpecResults_NonTargetAnalysis>) plot_groups_profile(<MassSpecResults_NonTargetAnalysis>) get_groups_ms1(<MassSpecResults_NonTargetAnalysis>) get_groups_ms2(<MassSpecResults_NonTargetAnalysis>) plot_groups_ms1(<MassSpecResults_NonTargetAnalysis>) plot_groups_ms2(<MassSpecResults_NonTargetAnalysis>) get_components(<MassSpecResults_NonTargetAnalysis>) map_components(<MassSpecResults_NonTargetAnalysis>) get_suspects(<MassSpecResults_NonTargetAnalysis>) plot_suspects(<MassSpecResults_NonTargetAnalysis>) get_internal_standards(<MassSpecResults_NonTargetAnalysis>) plot_internal_standards(<MassSpecResults_NonTargetAnalysis>) get_compounds(<MassSpecResults_NonTargetAnalysis>) get_fold_change(<MassSpecResults_NonTargetAnalysis>) plot_fold_change(<MassSpecResults_NonTargetAnalysis>) get_patRoon_features(<MassSpecResults_NonTargetAnalysis>) get_patRoon_MSPeakLists(<MassSpecResults_NonTargetAnalysis>) get_patRoon_compounds(<MassSpecResults_NonTargetAnalysis>): Constructor and methods to handle non-target analysis results for mass spectrometry data

MassSpecResults_Spectra() validate_object(<MassSpecResults_Spectra>) show(<MassSpecResults_Spectra>) `[`(<MassSpecResults_Spectra>) get_spectra(<MassSpecResults_Spectra>) plot_spectra(<MassSpecResults_Spectra>) plot_spectra_3d(<MassSpecResults_Spectra>) plot_spectra_charges(<MassSpecResults_Spectra>) get_spectra_matrix(<MassSpecResults_Spectra>) get_spectra_peaks(<MassSpecResults_Spectra>) plot_spectra_peaks(<MassSpecResults_Spectra>): Constructor and methods to handle mass spectrometry spectra results

Raman Spectroscopy Results

RamanResults_Spectra() validate_object(<RamanResults_Spectra>) show(<RamanResults_Spectra>) `[`(<RamanResults_Spectra>) `[[`(<RamanResults_Spectra>): Constructor and methods to handle Raman spectra results

RamanResults_SpectraSimilarity() validate_object(<RamanResults_SpectraSimilarity>) show(<RamanResults_SpectraSimilarity>): Constructor and methods to handle Raman spectra similarity results

Statistical Analyses Results

StatisticResults_KNN_class() validate_object(<StatisticResults_KNN_class>) get_model_data(<StatisticResults_KNN_class>) test(<StatisticResults_KNN_class>) predict(<StatisticResults_KNN_class>): StatisticResults_KNN_class Class

StatisticResults_MCRALS_mdatools() validate_object(<StatisticResults_MCRALS_mdatools>) summary(<StatisticResults_MCRALS_mdatools>) predict(<StatisticResults_MCRALS_mdatools>) test(<StatisticResults_MCRALS_mdatools>) get_model_data(<StatisticResults_MCRALS_mdatools>) plot_explained_variance(<StatisticResults_MCRALS_mdatools>) plot_cumulative_explained_variance(<StatisticResults_MCRALS_mdatools>) plot_resolved_spectra(<StatisticResults_MCRALS_mdatools>) plot_contributions(<StatisticResults_MCRALS_mdatools>) plot_overview(<StatisticResults_MCRALS_mdatools>): StatisticResults_MCRALS_mdatools Class

StatisticResults_MCRPURE_mdatools() validate_object(<StatisticResults_MCRPURE_mdatools>) summary(<StatisticResults_MCRPURE_mdatools>) plot_overview(<StatisticResults_MCRPURE_mdatools>) get_model_data(<StatisticResults_MCRPURE_mdatools>) predict(<StatisticResults_MCRPURE_mdatools>) test(<StatisticResults_MCRPURE_mdatools>) plot_explained_variance(<StatisticResults_MCRPURE_mdatools>) plot_cumulative_explained_variance(<StatisticResults_MCRPURE_mdatools>) plot_resolved_spectra(<StatisticResults_MCRPURE_mdatools>) plot_contributions(<StatisticResults_MCRPURE_mdatools>): StatisticResults_MCRPURE_mdatools Class

StatisticResults_Model() validate_object(<StatisticResults_Model>) show(<StatisticResults_Model>): StatisticResults_Model Class

StatisticResults_PCA_mdatools() validate_object(<StatisticResults_PCA_mdatools>) summary(<StatisticResults_PCA_mdatools>) get_model_data(<StatisticResults_PCA_mdatools>) predict(<StatisticResults_PCA_mdatools>) test(<StatisticResults_PCA_mdatools>) plot_explained_variance(<StatisticResults_PCA_mdatools>) plot_cumulative_explained_variance(<StatisticResults_Model>) plot_scores(<StatisticResults_PCA_mdatools>) plot_loadings(<StatisticResults_PCA_mdatools>) plot_residuals(<StatisticResults_PCA_mdatools>) plot_residual_distance(<StatisticResults_PCA_mdatools>) plot_overview(<StatisticResults_PCA_mdatools>): StatisticResults_PCA_mdatools Class

Configuration (S3)

Configuration is governed by Config class which consists of a list of ConfigParameter class objects. Childs of both Config and ConfigParameter classes are implemented for specific use cases.

AppConfig(): App Configuration

Config() validate_object(<Config>) show(<Config>) as.data.table(<Config>): Generic Configuration

ConfigCache() validate_object(<ConfigCache>) size(<ConfigCache>) info(<ConfigCache>): Configuration Parameter for Caching

ConfigDurationNotifications() validate_object(<ConfigDurationNotifications>): Configuration Parameter for Duration of Notifications

ConfigExtraRoots() validate_object(<ConfigExtraRoots>): Configuration Parameter for Extra Root Directories

ConfigParameter() validate_object(<ConfigParameter>): ConfigParameter S3 Class

EngineConfig(): Engine Configuration

Audit Trail (S3)

Audit trail is governed by a specific class, registering all changes made to the data within an Engine.

AuditTrail() validate_object(<AuditTrail>) add(<AuditTrail>) as.data.table(<AuditTrail>) show(<AuditTrail>) save(<AuditTrail>) read(<AuditTrail>): Audit Trail Register

AuditTrailEntry() validate_object(<AuditTrailEntry>): Generic Entry for Audit Trail

Other Functions

convert_ms_files(): Function to convert vendor MS files to mzML or mzXML

trim_ms_files_spectra(): Function to trim spectra in mzML or mzXML files

run_app(): Run the Shiny Application