clueGO to R

[Roy Francis]

The data exported from clueGO in Cytoscape could be cleaned up as it is messy. I was hoping I could read the network from cytoscape into R to do some data clean up. Anyone know to import network from Cytoscape to R?

I have tried `read.graph()` from `igraph` but it returns an error.

library(igraph)
b <- read.graph("sample.graphml",format="graphml")


Error in .Call("R_igraph_read_graph_graphml", file, as.numeric(index),  :
  At rinterface.c:5866 : Cannot open GraphML file, File operation error

Thanks,

Roy

[Barry Demchak]

Roy –

 

This looks like a good application of cyREST, which is built into Cytoscape as of v3.4

 

Here is the app documentation that goes with it: http://apps.cytoscape.org/apps/cyrest

 

Here is a paper that describes its use in Python and R: http://f1000research.com/articles/4-478/v1

 

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Roy Francis
Sent: Monday, August 15, 2016 1:24 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] clueGO to R

 

The data exported from clueGO in Cytoscape could be cleaned up as it is messy. I was hoping I could read the network from cytoscape into R to do some data clean up. Anyone know to import network from Cytoscape to R?

Thanks,

Roy

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