NetSimplify: PPI network simplification
In fairmiracle/PPINet: Protenin-protein interaction network construction and module identification
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$Edgelist,num_iter=1000, muCh=0.05, zToR=10, minsize=10)
fairmiracle/PPINet documentation built on May 16, 2019, 9:59 a.m.
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Description Usage Arguments Value Author(s) See Also Examples
Description
Simplify protenin-protein interaction network, for module identification
Usage
1 | NetSimplify(net, p.values, STRINGTheta = 0)
|
Arguments
net |
Edgelist from |
p.values |
The p-values vector |
savename |
Name for saving PPI edge list as plain file and also saving nodes in largest connected component and figure as eps format by default |
Value
a list containing module size, best score, module as a list of nodes
Author(s)
Dong Li, dxl466@cs.bham.ac.uk
See Also
PPIFromString, PPIFromStringEnsembl
and PPIFromBioGRID
Examples
1 2 3 4 | require(genalg)
Sp <- NetSimplify(net,0)
GA_result <- GA_search_connected(lambda=0.5,Sp$node_score,Sp$edge_score,
Sp$Edgelist,num_iter=1000, muCh=0.05, zToR=10, minsize=10)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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