workflowStep-class: (Virtual) Base class for all workflow objects.

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

(Virtual) Base class for all workflow objects.

Description

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 signature 'workflowStep'
algorithm(obj)

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

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

## S4 method for signature '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

      • transformationProductsBT

      • transformationProductsLibrary

    • transformationProductsFormula

      • transformationProductsLibraryFormula

    • transformationProductsLogic

  • features

    • featuresSet

    • featuresUnset

    • featuresFromFeatGroups

    • featuresConsensus

    • featuresBruker

    • featuresEnviPick

    • featuresKPIC2

    • featuresOpenMS

    • featuresSAFD

    • featuresSIRIUS

    • featuresBrukerTASQ

    • featuresXCMS

    • featuresXCMS3

  • featureGroups

    • featureGroupsSet

      • featureGroupsScreeningSet

    • featureGroupsUnset

    • featureGroupsScreening

      • featureGroupsSetScreeningUnset

    • featureGroupsBruker

    • featureGroupsConsensus

    • featureGroupsEnviMass

    • featureGroupsKPIC2

    • featureGroupsOpenMS

    • featureGroupsSIRIUS

    • featureGroupsBrukerTASQ

    • featureGroupsXCMS

    • featureGroupsXCMS3

  • components

    • componentsCamera

    • componentsFeatures

      • componentsCliqueMS

      • componentsOpenMS

    • componentsClust

      • componentsIntClust

      • componentsSpecClust

    • componentsSet

      • componentsNTSet

    • componentsUnset

    • componentsNT

      • componentsNTUnset

    • componentsRC

    • componentsTPs

  • featureAnnotations

    • formulas

      • formulasConsensus

      • formulasSet

      • formulasUnset

      • formulasSIRIUS

    • compounds

      • compoundsConsensus

      • compoundsMF

      • compoundsSet

      • compoundsUnset

      • compoundsSIRIUS

  • MSPeakLists

    • MSPeakListsSet

    • MSPeakListsUnset

  • MSLibrary

rickhelmus/patRoon documentation built on April 25, 2024, 8:15 a.m.