cluster_tuning: ClusterONE Hyperparameters Tuning

In MACP: Macromolecular Assemblies from Co-Elution Profile (MACP)

ClusterONE Hyperparameters Tuning

Description

This function optimizes the choice of ClusterONE algorithm parameters such as density, node penalty, and overlap score by comparing clustering-derived partitions for each combination of parameters to known labels (i.e., CORUM complexes) and assess the similarity between them using quality measures including overlap score, sensitivity (Sn), clustering-wise positive predictive value (PPV), geometric accuracy (Acc), and maximum matching raio (MMR).It is recommended to first reduce redundancy in the known reference complexes via EliminateCpxRedundance,then performs parameter tuning.

Usage

cluster_tuning(
  refcpx,
  csize = 2,
  d = c(0.3, 0.5),
  p = c(2),
  max_overlap = c(0.5, 0.6),
  tpath = file.path(system.file("extdata", package = "MACP"))
)

Arguments

refcpx	A list containing reference complexes (i.e., corum complexes).
csize	An integer, the minimum size of the predicted complexes. Defualts to 2.
d	A vector of number, density of predicted complexes.
p	A vector of integer, penalty value for the inclusion of each node.
max_overlap	A vector of number, specifies the maximum allowed overlap between two clusters.
tpath	A character string indicating the path to the project directory that contains the interaction data. Interaction data must be stored as .txt file and containing id1-id2-weight triplets. Defaults to MACP/inst/extdata directory.

Details

cluster_tuning

Value

A data.frame containing clustering performance across different combination of parameters.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

References

Nepusz, T., Yu, H., and Paccanaro, A. (2012a). Detecting overlapping protein complexes in protein-protein interaction networks. Nat. Methods 9, 471.

MACP documentation built on March 7, 2023, 7:42 p.m.