how to build Reactome.Symbol.Igraph for mouse?

[chengkeren]

Hi~
I found this packages is very interesting, and I am working on mouse, so how can I built a mouse Reactome.Symbol.Igraph?

Thanks

[AJEinstein]

The author who built the Reactome igraph is in the middle of his residency and hasn't been responsive. I would suggest using string's network igraph for mouse. See the STRINGdb package on bioconductor for more information. Briefly:

1. you need to download the mouse string data:

string_db <- STRINGdb$new(version="10", species=10090, score_threshold=0, input_directory="SMITE/StringDB")`

2. you would need to convert your gene ID's to string ID's (instead of gene symbols)

test_sym_2 <- string_db$map(exprs, "id", removeUnmappedRows = TRUE)`

3. Use the stringDB igraph in lieu of the reactome igraph

string_igraph <- string_db$get_graph()
test_annotation <- 
  runSpinglass(test_annotation, network = string_igraph, maxsize = 50,
               num_iterations = 1000)

I hope this helps. Sorry for the long long delay.