Direct interactions in graphite ?
1
@emisecherre-23089
Last seen 4.5 years ago
hello !
I'm trying to use graphite to extrat direct interactions between molecules (so, without any intermediate molecules). I tried this with Reactome, but when i checked interactions obtained with graphite in Reactome, i see only a few direct interactions on PathwayBrowser, not all graphite results. Is there a way to get only the interactions i want on graphite ?
graphite
interaction
• 1.1k views
@gabrielesales-6826
Last seen 3.1 years ago
European Union
You can extract direct interactions from a pathway making use of the "type" attribute of each edge.
Taking a Reactome pathway as an example:
> library( graphite)
> library( dplyr)
> hsa < - pathways( "hsapiens" , "reactome" )
> edges( hsa[ [ "Apoptosis" ] ] ) %> % filter( type== "Process(BiochemicalReaction)" )
src_type src dest_type dest direction type
1 UNIPROT P0CG47 UNIPROT Q13177 directed Process( BiochemicalReaction)
2 UNIPROT P0CG48 UNIPROT Q13177 directed Process( BiochemicalReaction)
3 UNIPROT P62979 UNIPROT Q13177 directed Process( BiochemicalReaction)
4 UNIPROT P62987 UNIPROT Q13177 directed Process( BiochemicalReaction)
5 UNIPROT Q13177 UNIPROT P0CG47 directed Process( BiochemicalReaction)
6 UNIPROT Q13177 UNIPROT P0CG48 directed Process( BiochemicalReaction)
7 UNIPROT Q13177 UNIPROT P62979 directed Process( BiochemicalReaction)
8 UNIPROT Q13177 UNIPROT P62987 directed Process( BiochemicalReaction)
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