(Virtual) Base class for all workflow objects.

All workflow objects (e.g. featureGroups, compounds, etc) are derived from this class. Objects from this class are never created directly.

Usage

# S4 method for class 'workflowStep'
algorithm(obj)

# S4 method for class 'workflowStep'
as.data.table(x, keep.rownames = FALSE, ...)

# S4 method for class 'workflowStep'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

# S4 method for class 'workflowStep'
show(object)

Arguments

obj, x, object

An object (derived from) this class.

keep.rownames

Ignored.

...

Method specific arguments. Please see the documentation of the derived classes.

row.names, optional

Ignored.

Methods (by generic)

• algorithm(workflowStep): Returns the algorithm that was used to generate an object.

• as.data.table(workflowStep): Summarizes the data in this object and returns this as a data.table.

• as.data.frame(workflowStep): This method simply calls as.data.table and converts the result to a classic a data.frame.

• show(workflowStep): Shows summary information for this object.

Slots

algorithm

The algorithm that was used to generate this object. Use the algorithm method for access.

S4 class hierarchy

• workflowStep

  • transformationProducts

    • transformationProductsStructure

      • transformationProductsStructureConsensus

      • transformationProductsCTS

      • transformationProductsAnnComp

      • transformationProductsBT

      • transformationProductsLibrary

    • transformationProductsFormula

      • transformationProductsAnnForm

      • transformationProductsLibraryFormula

    • transformationProductsLogic

  • features

    • featuresSet

    • featuresUnset

    • featuresFromFeatGroups

    • featuresConsensus

    • featuresBruker

    • featuresEnviPick

    • featuresKPIC2

    • featuresOpenMS

    • featuresPiek

    • featuresSAFD

    • featuresSIRIUS

    • featuresTable

    • featuresBrukerTASQ

    • featuresXCMS

    • featuresXCMS3

  • featureGroups

    • featureGroupsSet

      • featureGroupsScreeningSet

    • featureGroupsUnset

    • featureGroupsScreening

      • featureGroupsSetScreeningUnset

    • featureGroupsBruker

    • featureGroupsConsensus

    • featureGroupsEnviMass

    • featureGroupsGreedy

    • featureGroupsIMS

    • featureGroupsKPIC2

    • featureGroupsOpenMS

    • featureGroupsSIRIUS

    • featureGroupsTable

    • featureGroupsBrukerTASQ

    • featureGroupsXCMS

    • featureGroupsXCMS3

  • components

    • componentsCamera

    • componentsFeatures

      • componentsCliqueMS

      • componentsOpenMS

    • componentsClust

      • componentsIntClust

      • componentsSpecClust

    • componentsSet

      • componentsNetSet

      • componentsNTSet

    • componentsUnset

    • componentsNet

      • componentsNetUnset

    • componentsNT

      • componentsNTUnset

    • componentsRC

    • componentsTPs

  • featureAnnotations

    • formulas

      • formulasConsensus

      • formulasSet

      • formulasUnset

      • formulasSIRIUS

    • compounds

      • compoundsConsensus

      • compoundsMF

      • compoundsSet

      • compoundsUnset

      • compoundsSIRIUS

  • MSPeakLists

    • MSPeakListsSet

    • MSPeakListsUnset

  • MSLibrary