mcl_system_cmd: Call MCL program for graph partitioning (internal).

In dputhier/scigenex: The scigenex package (Single-Cell Informative GENe Explorer)

Call MCL program for graph partitioning (internal).

Description

Call MCL program for graph partitioning (internal).

Usage

mcl_system_cmd(
  object = NULL,
  inflation = inflation,
  threads = 1,
  mcl_dir = NULL
)

Arguments

object	a ClusterSet object.
inflation	numeric. The inflation parameter used to control the granularity of the clustering.
threads	integer. The number of threads to use.
mcl_dir	The directory were mcl is installed (guessed otherwise).

Details

This function call the MCL program for graph partitioning. MCL is a graph clustering algorithm that detects clusters of nodes in a graph based on the flow of information through the edges. It is a fast and efficient algorithm that can be used for clustering large-scale graphs.

Value

a ClusterSet object with the updated parameters.

Warnings

With the current implementation, this function only works only on UNIX-like plateforms.

MCL should be installed. Run the install_mcl command to install it.

References

- Van Dongen S. (2000) A cluster algorithm for graphs. National Research Institute for Mathematics and Computer Science in the 1386-3681.

dputhier/scigenex documentation built on April 17, 2025, 4:43 a.m.