fetchGrinnNetwork

This example shows how to reconstruct a biological network (grinn network) using information from Grinn internal database

1. INPUT
   

   The table summarizes important arguments

   Argument	Value	Description
   txtInput	list of keywords e.g. ENSG00000143811	Keywords are IDs from a specific database.
   from	type of keyword e.g. metabolite	Type of starting points in the network. It can be one of metabolite, protein, gene, pathway.
   to	type of end nodes e.g. pathway	Type of endpoints in the network. It can be one of metabolite, protein, gene, pathway.
   dbXref	database name e.g. kegg	Database name used for the keywords ids. It can be one of grinn, chebi, kegg, pubchem, inchi, hmdb, smpdb, reactome, uniprot, ensembl, entrezgene.



2. EXECUTE FUNCTION
   

   Build a grinn network of gene-protein-metabolite using the list of ENSEMBL genes

   
   txtInput <- list('ENSG00000140459','ENSG00000143811','ENSG00000104524')
   result <- fetchGrinnNetwork(txtInput, from="gene", to="metabolite", returnAs="tab", dbXref="ensembl")
   #display the first 10 edgelists
   result$edges[1:10,]
                 

3. EXPORT OUTPUT
   

   Export the network as tab-delimited files to visualize in Cytoscape

   
   write.table(as.matrix(result$edges),"grinnNwEdge.txt",sep="\t",row.names = F, quote = FALSE)
   write.table(as.matrix(result$nodes),"grinnNwNode.txt",sep="\t",row.names = F, quote = FALSE)
                 

4. VISUALIZATION

   The figure is generated by Cytoscape 3.1.1 using grinn style (grinn.xml). It is corresponding to the cytoscape file grinnNw.cys.




Diagram legend

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