Export adjacency matrix to cytoscape
I have an RNA-seq dataset that I am analyzing for gene-network analysis. I'm loosely following the tutorial for this here: github.com/iscb-dc-rsg/2016-summer-workshop/blob/master/3B-Hughitt-RNASeq-Coex-Network-Analysis/tutorial/README.md
I'm using my own data which deals with a non-model organism, and so I've had trouble adapting the code to suit my needs. Since I cannot associate my data with an annotation package (unless there's one for Oreochromis niloticus that I haven't found!) I haven't been able to export the matrix in GML format for cytoscape.
This is the last step I have reached below (creating matrix format)
Co-expression network construction -- was able to create similarity matrix and convert to adjacency matrix. Also created Co-expression module detection. I just can't export the network.
g <- export_network_to_graphml(adj_matrix, filename="~/network.graphml", threshold =0.4)
This doesn't work because the 'nodeAttrDataFrame' argument in the function is missing. I've tried modifying the function in the tutorial to remove this argument but it also doesn't fully work. It creates an object in my environment, but does not save to my computer. Here is also what I tried:
write_graph(g, "~/network.graphml", format ="gml")
Any help would be appreciated!
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