Function reference • StreamFind

Data Processing Engines

R6 classes are used as processing engines for reading, processing, inspecting and storing data.

CoreEngine: CoreEngine R6 class and methods

MassSpecEngine: MassSpecEngine R6 class and methods

RamanEngine: RamanEngine R6 class and methods

StatisticEngine: StatisticEngine R6 class and methods

Project Headers

The ProjectHeaders S3 class is used to store, assign and dispatch the project headers to the processing engines.

ProjectHeaders(): ProjectHeaders S3 class constructor, methods and functions

Analysis

The Analysis S3 class and data dedicated childs are used to store, assign and dispatch the analysis data to the processing engines.

Analysis(): Analysis S3 class constructor, methods and functions

MassSpecAnalysis(): MassSpecAnalysis S3 class constructor, methods and functions

RamanAnalysis(): RamanAnalysis S3 class constructor, methods and functions

StatisticAnalysis(): StatisticAnalysis S3 class constructor, methods and functions

Processing settings

The ProcessingSettings S3 class is used to store, assign and dispatch the algorithm and respective parameters to processing methods. The ProcessingSettings object obtains a subclass according to the assinged algorithm for each engine and processing method. Below the available subclasses for ProcessingSettings are listed for each type of processing engine.

ProcessingSettings(): ProcessingSettings S3 class constructor, methods and functions

MassSpec Settings

MassSpecSettings_AnnotateFeatures_StreamFind(): MassSpecSettings_AnnotateFeatures_StreamFind

MassSpecSettings_AverageSpectra_StreamFind(): MassSpecSettings_AverageSpectra_StreamFind

MassSpecSettings_BinSpectra_StreamFind(): MassSpecSettings_BinSpectra_StreamFind

MassSpecSettings_CalculateQuality_StreamFind(): MassSpecSettings_CalculateQuality_StreamFind

MassSpecSettings_CalculateSpectraCharges_StreamFind(): MassSpecSettings_CalculateSpectraCharges_StreamFind

MassSpecSettings_CentroidSpectra_qCentroids(): MassSpecSettings_CentroidSpectra_qCentroids

MassSpecSettings_ClusterSpectra_StreamFind(): MassSpecSettings_ClusterSpectra_StreamFind

MassSpecSettings_CorrectChromatogramsBaseline_airpls(): MassSpecSettings_CorrectChromatogramsBaseline_airpls

MassSpecSettings_CorrectChromatogramsBaseline_baseline(): MassSpecSettings_CorrectChromatogramsBaseline_baseline

MassSpecSettings_CorrectSpectraBaseline_airpls(): MassSpecSettings_CorrectSpectraBaseline_airpls

MassSpecSettings_CorrectSpectraBaseline_baseline(): MassSpecSettings_CorrectSpectraBaseline_baseline

MassSpecSettings_DeconvoluteSpectra_StreamFind(): MassSpecSettings_DeconvoluteSpectra_StreamFind

MassSpecSettings_FillFeatures_StreamFind(): MassSpecSettings_FillFeatures_StreamFind

MassSpecSettings_FilterFeatures_patRoon(): MassSpecSettings_FilterFeatures_patRoon

MassSpecSettings_FilterFeatures_StreamFind(): MassSpecSettings_FilterFeatures_StreamFind

MassSpecSettings_FindFeatures_kpic2(): MassSpecSettings_FindFeatures_kpic2

MassSpecSettings_FindFeatures_openms(): MassSpecSettings_FindFeatures_openms

MassSpecSettings_FindFeatures_qPeaks(): MassSpecSettings_FindFeatures_qPeaks

MassSpecSettings_FindFeatures_xcms3_centwave(): MassSpecSettings_FindFeatures_xcms3_centwave

MassSpecSettings_FindFeatures_xcms3_matchedfilter(): MassSpecSettings_FindFeatures_xcms3_matchedfilter

MassSpecSettings_FindInternalStandards_StreamFind(): MassSpecSettings_FindInternalStandards_StreamFind

MassSpecSettings_GenerateCompounds_metfrag(): MassSpecSettings_GenerateCompounds_metfrag

MassSpecSettings_GenerateFormulas_genform(): MassSpecSettings_GenerateFormulas_genform

MassSpecSettings_GroupFeatures_openms(): MassSpecSettings_GroupFeatures_openms

MassSpecSettings_GroupFeatures_xcms3_peakdensity(): MassSpecSettings_GroupFeatures_xcms3_peakdensity

MassSpecSettings_GroupFeatures_xcms3_peakdensity_peakgroups(): MassSpecSettings_GroupFeatures_xcms3_peakdensity_peakgroups

MassSpecSettings_IntegrateChromatograms_StreamFind(): MassSpecSettings_IntegrateChromatograms_StreamFind

MassSpecSettings_LoadFeaturesEIC_StreamFind(): MassSpecSettings_LoadFeaturesEIC_StreamFind

MassSpecSettings_LoadFeaturesMS1_StreamFind(): MassSpecSettings_LoadFeaturesMS1_StreamFind

MassSpecSettings_LoadFeaturesMS2_StreamFind(): MassSpecSettings_LoadFeaturesMS2_StreamFind

MassSpecSettings_LoadMSPeakLists_patRoon(): MassSpecSettings_LoadMSPeakLists_patRoon

MassSpecSettings_LoadMSPeakLists_StreamFind(): MassSpecSettings_LoadMSPeakLists_StreamFind

MassSpecSettings_NormalizeSpectra_blockweight(): MassSpecSettings_NormalizeSpectra_blockweight

MassSpecSettings_NormalizeSpectra_meancenter(): MassSpecSettings_NormalizeSpectra_meancenter

MassSpecSettings_NormalizeSpectra_minmax(): MassSpecSettings_NormalizeSpectra_minmax

MassSpecSettings_NormalizeSpectra_scale(): MassSpecSettings_NormalizeSpectra_scale

MassSpecSettings_NormalizeSpectra_snv(): MassSpecSettings_NormalizeSpectra_snv

MassSpecSettings_SmoothChromatograms_movingaverage(): MassSpecSettings_SmoothChromatograms_movingaverage

MassSpecSettings_SmoothChromatograms_savgol(): MassSpecSettings_SmoothChromatograms_savgol

MassSpecSettings_SmoothSpectra_movingaverage(): MassSpecSettings_SmoothSpectra_movingaverage

MassSpecSettings_SmoothSpectra_savgol(): MassSpecSettings_SmoothSpectra_savgol

MassSpecSettings_SubtractBlankSpectra_StreamFind(): MassSpecSettings_SubtractBlankSpectra_StreamFind

MassSpecSettings_SuspectScreening_forident(): MassSpecSettings_SuspectScreening_forident

MassSpecSettings_SuspectScreening_patRoon(): MassSpecSettings_SuspectScreening_patRoon

MassSpecSettings_SuspectScreening_StreamFind(): MassSpecSettings_SuspectScreening_StreamFind

Raman Settings

RamanSettings_AverageSpectra_StreamFind(): RamanSettings_AverageSpectra_StreamFind

RamanSettings_BinSpectra_StreamFind(): RamanSettings_BinSpectra_StreamFind

RamanSettings_CorrectSpectraBaseline_airpls(): RamanSettings_CorrectSpectraBaseline_airpls

RamanSettings_CorrectSpectraBaseline_baseline(): RamanSettings_CorrectSpectraBaseline_baseline

RamanSettings_DeleteSpectraSection_StreamFind(): RamanSettings_DeleteSpectraSection_StreamFind

RamanSettings_MergeSpectraTimeSeries_StreamFind(): RamanSettings_MergeSpectraTimeSeries_StreamFind

RamanSettings_NormalizeSpectra_blockweight(): RamanSettings_NormalizeSpectra_blockweight

RamanSettings_NormalizeSpectra_meancenter(): RamanSettings_NormalizeSpectra_meancenter

RamanSettings_NormalizeSpectra_minmax(): RamanSettings_NormalizeSpectra_minmax

RamanSettings_NormalizeSpectra_scale(): RamanSettings_NormalizeSpectra_scale

RamanSettings_NormalizeSpectra_snv(): RamanSettings_NormalizeSpectra_snv

RamanSettings_SmoothSpectra_movingaverage(): RamanSettings_SmoothSpectra_movingaverage

RamanSettings_SmoothSpectra_savgol(): RamanSettings_SmoothSpectra_savgol

RamanSettings_SubtractBlankSpectra_StreamFind(): RamanSettings_SubtractBlankSpectra_StreamFind

RamanSettings_SubtractSpectraSection_StreamFind(): RamanSettings_SubtractSpectraSection_StreamFind

Statistic Settings

StatisticSettings_MakeModel_mcrals_mdatools(): StatisticSettings_MakeModel_mcrals_mdatools

StatisticSettings_MakeModel_mcrpure_mdatools(): StatisticSettings_MakeModel_mcrpure_mdatools

StatisticSettings_MakeModel_pca_mdatools(): StatisticSettings_MakeModel_pca_mdatools

StatisticSettings_PrepareClassification_knn(): StatisticSettings_PrepareClassification_knn

General get and save default settings

Funtions to uniformily get and save ProcessingSettings are available. These return the default ProcessingSettings according the arguments call and algorithm.

get_default_ProcessingSettings(): get_default_ProcessingSettings

save_default_ProcessingSettings(): save_default_ProcessingSettings

S3 Generics

validate(): Validate

Other MS 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

import_MassSpecEngine(): Function to import a MassSpecEngine class object from a json or rds file.

combine_MassSpecEngine(): Function to combine MassSpecEngine class objects.

make_ms_targets(): Function to make targets for parsing data within MassSpecData class methods

clear_cache(): clear_cache