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ModuleGraph - Documentation

Contents

• Network
• Visual Style


• Module Data
• Defining new Modules and Importing Module Data
• Save and Load Module Data
• Display Module Data


• Module Scores
• Module Representation Score
• Module Connectivity Score

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Module Scores

To calculate the module scores in a ModuleGraph network choose ModuleGraph -> Compute Module Scores. The module representation score and the module connectivity score are then calculated w.r.t. the currently loaded module data and the current network. Both scores are stored as node attributes in Cytoscape and can be inspected in the node attribute browser. Further information and formal definitions can be found in the following sections.

Module Representation Score

The module representation score (MRS) reflects how well a module is represented in the network. More specificly, the MRS of module m is the fraction of elements of m present in the network. The total number of elements of m is determined by its definition in the module data.

, where V is the set of all nodes in the network.

Module Connectivity Score

The module connectivity score (MCS) reflects how well a module is connected. More specificly, the MCS of module m is the fraction of edges between elements of m in the network w.r.t. the maximum possible number of edges between elements of m in the network.

, where E and V are the sets of all edges and all nodes in the network, respectively.

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