generateComponentsSpecClust: Generate components based on MS/MS similarity

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

Generate components based on MS/MS similarity

Description

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

Usage

generateComponentsSpecClust(fGroups, ...)

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

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.

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.

Value

The components are stored in objects derived from componentsSpecClust.

Sets workflows

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

Author(s)

Rick Helmus <[e-mail]> and Bas van de Velde (major contributions to spectral binning and similarity calculation).

References

\addCitations

fastcluster1

See Also

generateComponents for more details and other algorithms.

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