Given a GRanges object with metadata columns related to the classification performed with the cluster_peak method, this function quantifies the elbow rule. See Details for a short presentation of the method and the Vignette of the package for a complete defintion of the index.
GRanges object. It must contain the metadata columns associated to the classification to be analyzed.
Specifically it must contain the
This function consists of the computation for each feasible value of k (from 2 to K ??? 1, with K the maximum number of clusters) of an index that quantifies the magnitude of the elbow. As higher is this index, as the correspondent value of k is meaningful. Specifically it is computed as the distance of the point in k of the global distance function (normalized with the maximum value it assumes) from the line passing by the point in k ??? 1 and in k + 1. For further details, see the Vignette.
The function returns
a data.frame (or a list with two data.frames, in case of
object with classification with and without alignment) containing the bending index for different values of the parameter k.
plot.graph.k = TRUE the graphical representation of the distances (normalized with the total number of peaks n), varying the classification type and the number of clusters.
Alice Parodi, Marco J. Morelli, Laura M. Sangalli, Piercesare Secchi, Simone Vantini
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