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Generate components based on MS/MS similarity

Source: R/generics.R, R/components-specclust.R
generateComponentsSpecClust.Rd

Generates components based on MS/MS similarity between feature groups.

Usage

generateComponentsSpecClust(fGroups, ...)

# S4 method for class 'featureGroups'
generateComponentsSpecClust(
  fGroups,
  MSPeakLists,
  method = "complete",
  specSimParams = getDefSpecSimParams(),
  maxTreeHeight = 1,
  deepSplit = TRUE,
  minModuleSize = 1,
  IMS = "maybe"
)

Arguments

fGroups

featureGroups object for which components should be generated.

...

Any parameters to be passed to the selected component generation algorithm.

MSPeakLists

The MSPeakLists object for the given feature groups that should be used for MS spectral similarity calculations.

method

Clustering method that should be applied (passed to fastcluster::hclust).

specSimParams

A named list with parameters that influence the calculation of MS spectra similarities. See the spectral similarity parameters documentation for more details.

maxTreeHeight, deepSplit, minModuleSize

Arguments used by cutreeDynamicTree.

IMS

(IMS workflow) Specifies which feature groups are considered for componentization in IMS workflows. The following options are valid:

  • "both": Selects IMS and non-IMS features.

  • "maybe": Selects non-IMS features and IMS features without assigned IMS precursor.

  • FALSE: Selects only non-IMS features.

  • TRUE: Selects only IMS features.

Value

The components are stored in objects derived from componentsSpecClust.

Details

This function uses hierarchical clustering of MS/MS spectra to generate components. This function is called when calling generateComponents with algorithm="specclust".

The similarities are converted to a distance matrix and used as input for hierarchical clustering, and the resulting dendrogram is automatically cut with cutreeDynamicTree. The clustering is performed with fastcluster::hclust.

IMS workflows

In IMS workflows with post mobility assignment (see assignMobilities) it may be necessary to call expandForIMS when componentization was performed prior to mobility assignments, see its documentation for more details.

If mobilities were already assigned prior to componentization, then the IMS argument selects which feature groups are subjected to componentization. Data for IMS feature groups that were not considered (i.e. when IMS is FALSE or "maybe"), will be expanded similarly as is done by expandForIMS.

Sets workflows

In a sets workflow the spectral similarities for each set are combined as is described for the spectrumSimilarity method for sets workflows.

References

Müllner D (2013). “fastcluster: Fast Hierarchical, Agglomerative Clustering Routines for R and Python.” Journal of Statistical Software, 53(9), 1–18. doi:10.18637/jss.v053.i09 .

See also

generateComponents for more details and other algorithms.

Author

Rick Helmus <r.helmus@uva.nl> and Bas van de Velde (major contributions to spectral binning and similarity calculation).