Package index • StreamFind

Introduction

StreamFind is built with two main class systems: R6 and S7. The R6 system is used for data processing engine classes, which are the main user interface for reading, processing, and inspecting different types of data. The S7 system is used for classes to manage metadata, analyses, data processing, results, audit trail and configuration. Below all classes exposed to the user are listed.

Engines (R6)

CoreEngine: Core Engine (Internal Use Only)

MassSpecEngine: Mass Spectrometry Engine

RamanEngine: Raman Spectroscopy Engine

StatisticEngine: Statistical Analysis Engine

Metadata (S7)

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

EngineMetadata(): Engine Metadata

Metadata(): Generic Metadata

Analyses (S7)

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(): Generic Analyses

MassSpecAnalyses(): Mass Spectrometry Analyses

RamanAnalyses(): Raman Spectroscopy Analyses

StatisticAnalyses(): Statistical Analyses (Tabular Data Input)

Data Processing (S7)

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(): Workflow Manager

ProcessingStep(): Generic Processing Step

Mass Spectrometry Methods

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

MassSpecMethod_AverageSpectra_StreamFind(): Mass Spectrometry Method for Averaging Spectra (StreamFind algorithm)

MassSpecMethod_BinSpectra_StreamFind(): Mass Spectrometry Method for Binning Spectra (StreamFind algorithm)

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

MassSpecMethod_CalculateSpectraCharges_native(): MassSpecMethod_CalculateSpectraCharges_native S7 class

MassSpecMethod_ClusterSpectra_StreamFind(): MassSpecMethod_ClusterSpectra_StreamFind S7 class

MassSpecMethod_CorrectChromatogramsBaseline_airpls(): MassSpecMethod_CorrectChromatogramsBaseline_airpls S7 class

MassSpecMethod_CorrectChromatogramsBaseline_baseline_als(): MassSpecMethod_CorrectChromatogramsBaseline_baseline_als S7 class

MassSpecMethod_CorrectMatrixSuppression_TiChri(): MassSpecMethod_CorrectMatrixSuppression_TiChri S7 class

MassSpecMethod_CorrectSpectraBaseline_airpls(): MassSpecMethod_CorrectSpectraBaseline_airpls S7 class

MassSpecMethod_CorrectSpectraBaseline_baseline_als(): MassSpecMethod_CorrectSpectraBaseline_baseline_als S7 class

MassSpecMethod_DeconvoluteSpectra_native(): MassSpecMethod_DeconvoluteSpectra_native S7 class

MassSpecMethod_FillFeatures_StreamFind(): MassSpecMethod_FillFeatures_StreamFind S7 class

MassSpecMethod_FilterChromPeaks_native(): MassSpecMethod_FilterChromPeaks_native S7 class

MassSpecMethod_FilterFeaturesMS2_native(): MassSpecMethod_FilterFeaturesMS2_native S7 class

MassSpecMethod_FilterFeatures_patRoon(): MassSpecMethod_FilterFeatures_patRoon S7 class

MassSpecMethod_FilterFeatures_StreamFind(): MassSpecMethod_FilterFeatures_StreamFind S7 class

MassSpecMethod_FindChromPeaks_LocalMaxima(): MassSpecMethod_FindChromPeaks_LocalMaxima S7 class

MassSpecMethod_FindChromPeaks_pracma(): MassSpecMethod_FindChromPeaks_pracma S7 class

MassSpecMethod_FindFeatures_kpic2(): MassSpecMethod_FindFeatures_kpic2 S7 class

MassSpecMethod_FindFeatures_openms(): MassSpecMethod_FindFeatures_openms S7 class

MassSpecMethod_FindFeatures_qalgorithms(): MassSpecMethod_FindFeatures_qalgorithms S7 class

MassSpecMethod_FindFeatures_xcms3_centwave(): MassSpecMethod_FindFeatures_xcms3_centwave S7 class

MassSpecMethod_FindFeatures_xcms3_matchedfilter(): MassSpecMethod_FindFeatures_xcms3_matchedfilter S7 class

MassSpecMethod_FindInternalStandards_StreamFind(): MassSpecMethod_FindInternalStandards_StreamFind S7 class

MassSpecMethod_FindSpectraMaxima_native(): MassSpecMethod_FindSpectraMaxima_native S7 class

MassSpecMethod_GenerateCompounds_metfrag(): MassSpecMethod_GenerateCompounds_metfrag S7 class

MassSpecMethod_GenerateFormulas_genform(): MassSpecMethod_GenerateFormulas_genform S7 class

MassSpecMethod_GroupFeatures_openms(): MassSpecMethod_GroupFeatures_openms S7 class

MassSpecMethod_GroupFeatures_xcms3_peakdensity(): MassSpecMethod_GroupFeatures_xcms3_peakdensity S7 class

MassSpecMethod_GroupFeatures_xcms3_peakdensity_peakgroups(): MassSpecMethod_GroupFeatures_xcms3_peakdensity_peakgroups S7 class

MassSpecMethod_IntegrateChromatograms_pracma(): MassSpecMethod_IntegrateChromatograms_pracma S7 class

MassSpecMethod_IntegrateSpectra_StreamFind(): MassSpecMethod_IntegrateSpectra_StreamFind S7 class

MassSpecMethod_LoadChromatograms_native(): MassSpecMethod_LoadChromatograms_native

MassSpecMethod_LoadFeaturesEIC_StreamFind(): MassSpecMethod_LoadFeaturesEIC_StreamFind S7 class

MassSpecMethod_LoadFeaturesMS1_StreamFind(): MassSpecMethod_LoadFeaturesMS1_StreamFind S7 class

MassSpecMethod_LoadFeaturesMS2_StreamFind(): MassSpecMethod_LoadFeaturesMS2_StreamFind S7 class

MassSpecMethod_LoadMSPeakLists_patRoon(): MassSpecMethod_LoadMSPeakLists_patRoon S7 class

MassSpecMethod_LoadMSPeakLists_StreamFind(): MassSpecMethod_LoadMSPeakLists_StreamFind S7 class

MassSpecMethod_LoadSpectra_chrompeaks(): MassSpecMethod_LoadSpectra_chrompeaks S7 class

MassSpecMethod_LoadSpectra_native(): MassSpecMethod_LoadSpectra_native S7 class

MassSpecMethod_NormalizeSpectra_blockweight(): MassSpecMethod_NormalizeSpectra_blockweight S7 class

MassSpecMethod_NormalizeSpectra_meancenter(): MassSpecMethod_NormalizeSpectra_meancenter S7 class

MassSpecMethod_NormalizeSpectra_minmax(): MassSpecMethod_NormalizeSpectra_minmax S7 class

MassSpecMethod_NormalizeSpectra_scale(): MassSpecMethod_NormalizeSpectra_scale S7 class

MassSpecMethod_NormalizeSpectra_snv(): MassSpecMethod_NormalizeSpectra_snv S7 class

MassSpecMethod_QuantifyChromatographicPeaks_native(): MassSpecMethod_QuantifyChromatographicPeaks_native S7 class

MassSpecMethod_SmoothChromatograms_movingaverage(): MassSpecMethod_SmoothChromatograms_movingaverage S7 class

MassSpecMethod_SmoothChromatograms_savgol(): MassSpecMethod_SmoothChromatograms_savgol S7 class

MassSpecMethod_SmoothSpectra_movingaverage(): MassSpecMethod_SmoothSpectra_movingaverage S7 class

MassSpecMethod_SmoothSpectra_savgol(): MassSpecMethod_SmoothSpectra_savgol S7 class

MassSpecMethod_SubtractBlankSpectra_StreamFind(): MassSpecMethod_SubtractBlankSpectra_StreamFind S7 class

MassSpecMethod_SuspectScreening_forident(): MassSpecMethod_SuspectScreening_forident S7 class

MassSpecMethod_SuspectScreening_patRoon(): MassSpecMethod_SuspectScreening_patRoon S7 class

MassSpecMethod_SuspectScreening_StreamFind(): MassSpecMethod_SuspectScreening_StreamFind S7 class

Raman Spectroscopy Methods

RamanMethod_AddShiftValues_native(): Raman Method for Adding Shift Values to Spectra (native algorithm)

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

RamanMethod_CalculateSpectraSimilary_hqi(): RamanMethod_CalculateSpectraSimilary_hqi

RamanMethod_CorrectSpectraBaseline_airpls(): RamanMethod_CorrectSpectraBaseline_airpls

RamanMethod_CorrectSpectraBaseline_baseline_als(): RamanMethod_CorrectSpectraBaseline_baseline_als

RamanMethod_DeleteScansSection_native(): RamanMethod_DeleteScansSection_native

RamanMethod_DeleteSpectraSection_native(): RamanMethod_DeleteSpectraSection_native

RamanMethod_FilterChromPeaks_native(): RamanMethod_FilterChromPeaks_native

RamanMethod_FilterSpectra_native(): RamanMethod_FilterSpectra_native

RamanMethod_FindChromPeaks_LocalMaxima(): RamanMethod_FindChromPeaks_LocalMaxima

RamanMethod_FindChromPeaks_pracma(): RamanMethod_FindChromPeaks_pracma

RamanMethod_GroupPeaks_native(): RamanMethod_GroupPeaks_native

RamanMethod_InvertAxis_intensity(): RamanMethod_InvertAxis_intensity

RamanMethod_MergeSpectraTimeSeries_StreamFind(): RamanMethod_MergeSpectraTimeSeries_StreamFind

RamanMethod_NormalizeSpectra_blockweight(): RamanMethod_NormalizeSpectra_blockweight

RamanMethod_NormalizeSpectra_meancenter(): RamanMethod_NormalizeSpectra_meancenter

RamanMethod_NormalizeSpectra_minmax(): RamanMethod_NormalizeSpectra_minmax

RamanMethod_NormalizeSpectra_scale(): RamanMethod_NormalizeSpectra_scale

RamanMethod_NormalizeSpectra_snv(): RamanMethod_NormalizeSpectra_snv

RamanMethod_RemoveCosmicRays_native(): RamanMethod_RemoveCosmicRays_native

RamanMethod_ScaleTime_native(): RamanMethod_ScaleTime_native

RamanMethod_SmoothSpectra_movingaverage(): RamanMethod_SmoothSpectra_movingaverage

RamanMethod_SmoothSpectra_savgol(): RamanMethod_SmoothSpectra_savgol

RamanMethod_SubtractBlankSpectra_StreamFind(): RamanMethod_SubtractBlankSpectra_StreamFind

RamanMethod_SubtractScansSection_native(): RamanMethod_SubtractScansSection_native

RamanMethod_SubtractSpectraSection_StreamFind(): RamanMethod_SubtractSpectraSection_StreamFind

Statistic Methods

StatisticMethod_MakeModel_knn(): StatisticMethod_MakeModel_knn S7 class

StatisticMethod_MakeModel_mcrals_mdatools(): StatisticMethod_MakeModel_mcrals_mdatools S7 class

StatisticMethod_MakeModel_mcrpure_mdatools(): StatisticMethod_MakeModel_mcrpure_mdatools S7 class

StatisticMethod_MakeModel_pca_mdatools(): StatisticMethod_MakeModel_pca_mdatools S7 class

StatisticMethod_PrepareData_autoscale(): StatisticMethod_PrepareData_autoscale

StatisticMethod_Quantify_mcrals(): Method for Quantification using an MCR-ALS model

Results (S7)

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.

NonTargetAnalysisResults(): Results class child for Non-target Analysis Workflows for Mass Spectrometry Data

Results(): Generic Results

Configuration (S7)

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(): Generic Configuration

ConfigCache(): Configuration Parameter for Caching

ConfigDurationNotifications(): Configuration Parameter for Duration of Notifications

ConfigExtraRoots(): Configuration Parameter for Extra Root Directories

ConfigParameter(): Generic Configuration Parameter

EngineConfig(): Engine Configuration

Audit Trail (S7)

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

AuditTrail(): Audit Trail Register

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

S7 Generics

Severeal S7 generics are used to define a common interface for a set of related functions. The behavior and possible arguments vary depending on the class of the object passed.

add(): Generic add

clear_cache(): Generic clear_cache

get_cache_info(): Generic get_cache_info

get_chromatograms(): Generic get_chromatograms

get_chromatograms_peaks(): Generic get_chromatograms_peaks

get_components(): Generic get_components

get_compounds(): Generic get_compounds

get_features(): Generic get_features

get_features_count(): Generic get_features_count

get_features_eic(): Generic get_features_eic

get_features_ms1(): Generic get_features_ms1

get_features_ms2(): Generic get_features_ms2

get_fold_change(): Generic get_fold_change

get_formulas(): Generic get_formulas

get_groups(): Generic get_groups

get_groups_ms1(): Generic get_groups_ms1

get_groups_ms2(): Generic get_groups_ms2

get_internal_standards(): Generic get_internal_standards

get_matrix_suppression(): Generic get_matrix_suppression

get_model_data(): Generic get_model_data

get_model_prediction(): Generic get_model_prediction

get_patRoon_compounds(): Generic get_patRoon_compounds

get_patRoon_features(): Generic get_patRoon_features

get_patRoon_MSPeakLists(): Generic get_patRoon_MSPeakLists

get_raw_chromatograms(): Generic get_raw_chromatograms

get_raw_spectra(): Generic get_raw_spectra

get_spectra(): Generic get_spectra

get_spectra_bpc(): Generic get_spectra_bpc

get_spectra_eic(): Generic get_spectra_eic

get_spectra_matrix(): Generic get_spectra_matrix

get_spectra_ms1(): Generic get_spectra_ms1

get_spectra_ms2(): Generic get_spectra_ms2

get_spectra_peaks(): Generic get_spectra_peaks

get_spectra_tic(): Generic get_spectra_tic

get_suspects(): Generic get_suspects

load(): Generic load

load_cache(): Generic load_cache

load_chromatograms(): Generic load_chromatograms

load_spectra(): Generic load_spectra

map_components(): Generic map_components

map_features(): Generic map_features

map_features_intensity(): Generic map_features_intensity

plot_chromatograms(): Generic plot_chromatograms

plot_chromatograms_baseline(): Generic plot_chromatograms_baseline

plot_chromatograms_peaks(): Generic plot_chromatograms_peaks

plot_components(): Generic plot_components

plot_contributions(): Generic plot_contributions

plot_cumulative_explained_variance(): Generic plot_cumulative_explained_variance

plot_data(): Generic plot_data

plot_explained_variance(): Generic plot_explained_variance

plot_features(): Generic plot_features

plot_features_count(): Generic plot_features_count

plot_features_eic(): Generic plot_features_eic

plot_features_ms1(): Generic plot_features_ms1

plot_features_ms2(): Generic plot_features_ms2

plot_fold_change(): Generic plot_fold_change

plot_groups(): Generic plot_groups

plot_groups_ms1(): Generic plot_groups_ms1

plot_groups_ms2(): Generic plot_groups_ms2

plot_groups_overview(): Generic plot_groups_overview

plot_groups_profile(): Generic plot_groups_profile

plot_internal_standards(): Generic plot_internal_standards

plot_loadings(): Generic plot_loadings

plot_matrix_suppression(): Generic plot_matrix_suppression

plot_residuals(): Generic plot_residuals

plot_residual_distance(): Generic plot_residual_distance

plot_resolved_spectra(): Generic plot_resolved_spectra

plot_scores(): Generic plot_scores

plot_spectra(): Generic plot_spectra

plot_spectra_3d(): Generic plot_spectra_3d

plot_spectra_baseline(): Generic plot_spectra_baseline

plot_spectra_bpc(): Generic plot_spectra_bpc

plot_spectra_charges(): Generic plot_spectra_charges

plot_spectra_eic(): Generic plot_spectra_eic

plot_spectra_ms1(): Generic plot_spectra_ms1

plot_spectra_ms2(): Generic plot_spectra_ms2

plot_spectra_peaks(): Generic plot_spectra_peaks

plot_spectra_tic(): Generic plot_spectra_tic

plot_spectra_xic(): Generic plot_spectra_xic

plot_suspects(): Generic plot_suspects

predict(): Generic predict

read(): Generic read

remove(): Generic remove

report(): Generic report

run(): Generic run

save(): Generic save

save_cache(): Generic save_cache

show(): Generic show

test(): Generic test