R/generics.R, R/components-specclust.R
generateComponentsSpecClust.RdGenerates components based on MS/MS similarity between feature groups.
generateComponentsSpecClust(fGroups, ...)
# S4 method for class 'featureGroups'
generateComponentsSpecClust(
fGroups,
MSPeakLists,
method = "complete",
specSimParams = getDefSpecSimParams(),
maxTreeHeight = 1,
deepSplit = TRUE,
minModuleSize = 1
)featureGroups object for which components should be generated.
Any parameters to be passed to the selected component generation algorithm.
The MSPeakLists object for the given feature groups that should be used for MS
spectral similarity calculations.
Clustering method that should be applied (passed to
fastcluster::hclust).
A named list with parameters that influence the calculation of MS spectra similarities.
See the spectral similarity parameters documentation for more details.
Arguments used by
cutreeDynamicTree.
The components are stored in objects derived from componentsSpecClust.
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.
In a sets workflow the spectral similarities for each set are
combined as is described for the spectrumSimilarity method
for sets workflows.
fastcluster1
generateComponents for more details and other algorithms.