NetSimplify: PPI network simplification

Description Usage Arguments Value Author(s) See Also Examples

Description

Simplify protenin-protein interaction network, for module identification

Usage

1
NetSimplify(net, p.values, STRINGTheta = 0)

Arguments

net

Edgelist from PPIFromString, PPIFromStringEnsembl and PPIFromBioGRID

p.values

The p-values vector

savename

Name for saving PPI edge list as plain file and also saving nodes in largest connected component and figure as eps format by default

Value

a list containing module size, best score, module as a list of nodes

Author(s)

Dong Li, dxl466@cs.bham.ac.uk

See Also

PPIFromString, PPIFromStringEnsembl and PPIFromBioGRID

Examples

1
2
3
4
require(genalg)
Sp <- NetSimplify(net,0)
GA_result <- GA_search_connected(lambda=0.5,Sp$node_score,Sp$edge_score,
Sp$Edgelist,num_iter=1000, muCh=0.05, zToR=10, minsize=10)

fairmiracle/PPINet documentation built on May 16, 2019, 9:59 a.m.