Miscellaneous generics

Source: R/generics.R

Various (S4) generic functions providing a common interface for common tasks such as plotting and filtering data. The actual functionality and function arguments are often specific for the implemented methods, for this reason, please refer to the linked method documentation for each generic.

adducts(obj, ...)

adducts(obj, ...) <- value

algorithm(obj)

analysisInfo(obj)

analyses(obj)

annotatedPeakList(obj, ...)

annotations(obj, ...)

calculatePeakQualities(obj, weights = NULL, flatnessFactor = 0.05, ...)

clusterProperties(obj)

clusters(obj)

consensus(obj, ...)

convertToMFDB(TPs, out, ...)

convertToSuspects(obj, ...)

cutClusters(obj)

defaultExclNormScores(obj)

export(obj, type, out, ...)

featureTable(obj, ...)

filter(obj, ...)

getBPCs(obj, ...)

getFeatures(obj)

getMCS(obj, ...)

getTICs(obj, ...)

groupNames(obj)

plotBPCs(obj, ...)

plotChord(obj, addSelfLinks = FALSE, addRetMzPlots = TRUE, ...)

plotChroms(obj, ...)

plotGraph(obj, ...)

plotInt(obj, ...)

plotScores(obj, ...)

plotSilhouettes(obj, kSeq, ...)

plotSpectrum(obj, ...)

plotStructure(obj, ...)

plotTICs(obj, ...)

plotVenn(obj, ...)

plotUpSet(obj, ...)

predictRespFactors(obj, ...)

predictTox(obj, ...)

delete(obj, ...)

plotVolcano(obj, ...)

replicateGroups(obj)

setObjects(obj)

sets(obj)

treeCut(obj, k = NULL, h = NULL, ...)

treeCutDynamic(
  obj,
  maxTreeHeight = 1,
  deepSplit = TRUE,
  minModuleSize = 1,
  ...
)

unset(obj, set)

Arguments

obj

The object the generic should be applied to.

...

Any further method specific arguments. See method documentation for details.

value

The replacement value.

weights, flatnessFactor

See method documentation.

TPs

The transformationProducts derived object.

out

Output file.

type

The export type.

If TRUE then 'self-links' are added which represent non-shared data.

addRetMzPlots

Set to TRUE to enable m/z vs retention time scatter plots.

kSeq

An integer vector containing the sequence that should be used for average silhouette width calculation.

k, h

Desired numbers of clusters. See cutree.

maxTreeHeight, deepSplit, minModuleSize

Arguments used by cutreeDynamicTree.

set

The name of the set.

Details

adducts returns assigned adducts of the object.

adducts<- sets adducts of the object.

algorithm returns the algorithm that was used to generate the object.

analysisInfo returns the analysis information from an object.

analyses returns a character vector with the analyses for which data is present in this object.

annotatedPeakList returns an annotated MS peak list.

annotations returns annotations.

calculatePeakQualities calculates chromatographic peak qualities and scores.

clusterProperties Obtain a list with properties of the generated cluster(s).

clusters Obtain clustering object(s).

consensus combines and merges data from various algorithms to generate a consensus.

convertToMFDB Exports the object to a local database that can be used with MetFrag.

  • Methods are defined for: .

convertToSuspects Converts an object to a suspect list.

cutClusters Returns assigned cluster indices of a cut cluster.

defaultExclNormScores Returns default scorings that are excluded from normalization.

export exports workflow data to a given format.

featureTable returns feature information.

filter provides various functionality to do post-filtering of data.

getBPCs gets base peak chromatogram(s).

getFeatures returns the object's features object.

getMCS Calculates the maximum common substructure.

getTICs gets total ion chromatogram(s).

groupNames returns a character vector with the names of the feature groups for which data is present in this object.

plotBPCs plots base peak chromatogram(s).

plotChord plots a Chord diagram to assess overlapping data.

plotChroms plots extracted ion chromatogram(s).

plotGraph Plots an interactive network graph.

plotInt plots the intensity of all contained features.

plotScores plots candidate scorings.

plotSilhouettes plots silhouette widths to evaluate the desired cluster size.

plotSpectrum plots a (annotated) spectrum.

plotStructure plots a chemical structure.

plotTICs plots total ion chromatogram(s).

plotVenn plots a Venn diagram to assess unique and overlapping data.

plotUpSet plots an UpSet diagram to assess unique and overlapping data.

predictRespFactors Prediction of response factors.

predictTox Prediction of toxicity values.

delete Deletes results.

plotVolcano plots a volcano plot.

replicateGroups returns a character vector with the analyses for which data is present in this object.

setObjects returns the set objects of this object. See the documentation of workflowStepSet.

sets returns the names of the sets inside this object. See the documentation for sets workflows.

treeCut Manually cut a cluster.

treeCutDynamic Automatically cut a cluster.

unset Converts this object to a regular non-set object. See the documentation for sets workflows.

Other generics

Below are methods that are defined for existing generics (e.g. defined in base). Please see method specific documentation for more details.

[ Subsets data within an object.

[[ Extract data from an object.

$ Extract data from an object.

as.data.table Converts an object to a table (data.table).

as.data.frame Converts an object to a table (data.frame).

length Returns the length of an object.

lengths Returns the lengths of elements within this object.

names Return names for this object.

plot Generates a plot for an object.

show Prints information about this object.