How to export a STRINGDB network to XML
1
0
Entering edit mode
Aditya ▴ 120
@aditya-7667
Last seen 7 months ago
Germany

Querying STRINGdb for a set of given gene names, and plotting the network works fine:

require(STRINGdb)
myDF <- data.frame(gene = c('AAAS', 'AACS', 'AAMP', 'AASS', 'ABCB7', 'ABCD4'))
mapped <- string_db$map(myDF, 'gene', removeUnmappedRows = TRUE)
string_db$plot_network(mapped$STRING_id)

Q: How to export this network to XML (for import into cytoscape)? I tried searching for such functionality, but couldn't find it:

STRINGdb$help("export")
ls('package:STRINGdb')
?`STRINGdb-class`
?`STRINGdb

 

STRINGdb • 1.0k views
ADD COMMENT
1
Entering edit mode
atariw ▴ 10
@atariw-7670
Last seen 22 months ago
Switzerland

Thankyou for using STRING.

Good question. We don't have such functionality at the moment (we take your suggestion into our wish list).

However a STRING network in R, is just an iGraph object (http://igraph.org).

With the function "get_subnetwork(string_ids)" you can obtain an iGraph object of the subnetwork generated with the STRING identifiers that you provide to the function.

Then you could in principle convert such iGraph object to a format that can be accepted by Cytoscape, or use plugins like (http://rcytoscape.systemsbiology.net).

ADD COMMENT
0
Entering edit mode

Very useful feedback, thanks a lot!

ADD REPLY

Login before adding your answer.

Traffic: 429 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6