This is a test version of Biostars. For the public version, visit https://www.biostars.org.
[Cytoscape] Merge nodes by column/attribute

Hi,

I have a network of protein - protein interactions, where the primary IDs of the nodes are Uniprot IDs. Now, some proteins can have different Uniprot IDs but share the same Gene Symbol, which I'm storing as an attribute in another column.

How can I merge nodes based on the value they have in the Gene Symbol attribute/column, while keeping all the edges of the original nodes?

I tried playing with Tools --> Merge --> Network but I can't get it to work (i.e.: nodes do not merge).

Any help is appreciated!

Thanks

merge node cytoscape id
• 4,144 views • link
updated by scooter scooter • written by enricoferrero enricoferrero

1 answer

Greetings,

If you go into the advanced options for Merge->Networks you should be able to set the matching columns of your two networks to the Gene Symbol. Make sure that the format of the Gene Symbol columns is the same, though (i.e. no quotes around one, no extra spaces in the other, etc.).

-- scooter

• 0 views • link
written by scooter scooter

Log in to answer this question.

More posts like this