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dhimmel / opcendo

Candidate OPC–endothelial cell interactors
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Expanding the interaction filter to include genes that match any or all GO IDs #4

Open dzoll opened 8 years ago

dzoll commented 8 years ago

Hi Daniel,

I would like to modify the interaction program so that, when adding multiple GO IDs, we can chose if the genes need to match all or only one of the GO IDS.

For example, I would like to expand my search of candidates to include protein A that is on the cell membrane of one cell, and protein B, that is in the extracellular matrix of the other. Using the GO ID for cell membrane would eliminate protein B from the results. Thus, setting the criteria that a gene can fit any of the filters (and not all) would allow us to identify more candidates.

Additionally, the ability to select between 'all' or 'any' would allow for more flexibility of the program.

dhimmel commented 8 years ago

You can now (991ac12da74952d7fe28eb3c33f89519221ee1f1) specify different GO Terms for the OPC candidate gene and the endo candidate gene.

You can switch between taking the intersection and union of GO terms by modifying the following lines of interaction.ipynb:

opc_go_subset = set.intersection(*[set(go_to_genes[term]) for term in opc_go_terms])
endo_go_subset = set.intersection(*[set(go_to_genes[term]) for term in endo_go_terms])