MCL_clustering: MCL clustering

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

MCL clustering

Description

This function applies MCL clustering to further refine the predicted subnetworks produced by ClusterONE.

Usage

MCL_clustering(hc_ppi, predcpx, inflation = 9, csize = 2)

Arguments

hc_ppi	High-confidence interactions data containing id1-id2-weight triplets.
predcpx	A data.frame containing predicted complexes resulted from get_clusters.
inflation	MCL inflation parameter. Defaults to 9.
csize	An integer, the minimum size of the predicted complexes. Defaults to 2.

Details

MCL_clustering

Value

List of refined complexes.

Author(s)

Matineh Rahmatbakhsh

Examples

# open high-confidence network
hc_ppi <-
read.delim(
system.file("extdata/ppi_input_ClusterONE.txt", package = "MACP"),
header = FALSE)
# predict complexes by ClusterONE
predcpx <-
get_clusters(csize = 3, d = 0.3, p = 2,
max_overlap = 0.8,
tpath = file.path(system.file("extdata", package = "MACP")))
# Break down big complexes by MCL
MCL_clusters <- MCL_clustering(hc_ppi, predcpx, inflation = 4, csize = 2)

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