ProNet (version 1.0.0)

mcode: MCODE network clustering

Description

Clustering of the network using the MCODE method.

Usage

mcode(graph, vwp = 0.5, haircut = FALSE, fluff = FALSE, fdt = 0.8, loops = TRUE)

Arguments

graph

An igraph object.

vwp

Vertex weight percentage. Default value is 0.5.

haircut

Boolean value, whether to remove singly-connected nodes from clusters (TRUE) or not (FALSE).

fluff

Boolean value, whether to spand cluster cores by one neighbour shell outwards (TRUE) or not (FALSE).

fdt

Cluster density cutoff. Default value is 0.8.

loops

Boolean value, whether to include self-loops (TRUE) or not (FALSE).

Value

A list of clusters.

References

Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics. 2003 Jan 13;4(1):2.

See Also

cluster

Examples

nlocal<-data.frame(c("DVL1","DVL2","DVL3"))
net<-construction(input=nlocal,db="HPRD",species="human",ID.type="Gene symbol",hierarchy=1)
mcode(net,vwp=0.9,haircut=TRUE,fluff=TRUE,fdt=0.1)