[CLOSED] node-centric network construction

[diffany-admin]

Issue by svlandeg Tue Sep 2 15:20:57 2014

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Building further upon #6, we need to first define the set of nodes that we will create differential networks for, to allow comparison across all conditions.

• start with DE genes < 0.05
• expand with PPI neighbours (exclude hubs? occurrence/percentage threshold?)
• expand with regulatory neighbours (exclude hubs, generic TFs, etc?)
• expand with DE genes < 0.1 which can still be connected to this network (and if high FC?)

--> take union of all nodes across all conditions, then go back and create all final edges for all conditions

[diffany-admin]

Comment by svlandeg Tue Sep 2 15:34:50 2014

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cf. NetworkConstruction.expandNetwork

[diffany-admin]

Comment by svlandeg Fri Sep 5 08:39:24 2014

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done: current form creates the reference network (no fold changes are encoded yet)