Remove Duplicated Edges behaviour

[Oana VIGY]

Dear All,

I have a question regarding the function "Remove Duplicated Edges" which deletes "edges that are complete duplicates, keeping one edge" (explanations from the user manual).

How are relations defined as "complete duplicates"? Is-it just relations between the same two nodes? even if the relation key is different?

I made simple tests (see attached) to try to understand the behaviour.

• [top of the picture] I have two proteins with 2 interactions defined as "ppi". In removing duplicates, one single edge is kept : ok
  
• [bottom of the picture] I have the same two proteins with interactions published in 2 different articles so I created different edge-keys (in "shared interaction"). In removing duplicates, one single edge is kept while for me, there are not duplicates.

I don't say it'a bug :-) I just want to understand how it works to use this feature in a good way.

Best regards,
Oana

[adam.t...@gladstone.ucsf.edu]

I've looked at the code, and the only comparison done to establish if the edges are duplicated is of the source and target node. (Direction is checked or ignored, as per the option in the dialog).   No attributes of the edges, such as the name, are considered in the operation.

It's fair to call this a bug.  In fact, its in our system here: http://code.cytoscape.org/redmine/issues/3343 

The complicating issue is that the command is not part of Cytoscape itself, it's in the NetworkAnalyzer app, and there is no set timeframe for when that might be revised.

Adam

[Oana VIGY]

Thanks Adam for having a look at that.

Have a good day,

Oana

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Oana VIGY

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