Question: Extract Graph Structure from WikiPathways into R igraph?
gravatar for areyoujokingme
4.7 years ago by
United States
areyoujokingme70 wrote:

I am tasked with the job of porting WikiPathways into an igraph object in R. I'm new to WikiPathways, and know about rWikiPathways R package, and have downloaded the .txt files of all human pathways.

I am also decently new to SPARQL, though it's reminiscent of SQL imho.

Basically, how would I go about approaching the goal of porting WikiPathways to R as an igraph object. I've looked into the .txt files, and they look like the below (see first 5 lines of an example file below). There is no edge (connections) information in these files, from what I can tell - just "node" declarations.

Identifier  Database
624 Entrez Gene
5972    Entrez Gene
1585    Entrez Gene
1511    Entrez Gene

Any help will be invaluable to me!

igraph wikipathways R • 1.2k views
ADD COMMENTlink written 4.7 years ago by areyoujokingme70
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