get_clusters: Predict Complexes

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

Predict Complexes

Description

This function partitions high-confidence network to putative complexes via ClusterONE clustering algorithm to identify protein complex membership.

Usage

get_clusters(
  csize = 2,
  d = 0.3,
  p = 2,
  max_overlap = 0.8,
  tpath = file.path(system.file("extdata", package = "MACP"))
)

Arguments

csize	An integer, the minimum size of the predicted complexes. Defaults to 2.
d	A number, density of predicted complexes. Defaults to 0.3.
p	An integer, penalty value for the inclusion of each node. Defaults to 2.
max_overlap	A number, specifies the maximum allowed overlap between two clusters. Defaults to 0.8.
tpath	A character string indicating the path to the project directory that contains the interaction data. Interactions data must be stored as .txt file and containing id1-id2-weight triplets.

Details

get_clusters

Value

A data.frame containing predicted complexes

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.

Examples

predcpx <-
get_clusters(csize = 3, d = 0.3, p = 2,
max_overlap = 0.8,
tpath = file.path(system.file("extdata", package = "MACP")))

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