Question: Is there anyway to get BioGrid gene interaction network automatically using R?
2
gravatar for Na Sed
5.0 years ago by
Na Sed280
United States
Na Sed280 wrote:

Is there anyway to get BioGrid gene interaction network automatically using R?

ADD COMMENTlink modified 5.0 years ago by Rajarshi Guha880 • written 5.0 years ago by Na Sed280
4
gravatar for Rajarshi Guha
5.0 years ago by
Rajarshi Guha880
United States
Rajarshi Guha880 wrote:

Coincidence! I've just been putting together an R client for BioGRID. Very rough initial version is at https://github.com/rajarshi/cdkr/tree/master/rbiogrid. To install 

library(devtools)
install_github("cdkr", "rajarshi", subdir="rbiogrid")

You will need to get an access key from the BioGRID website. Right now it has no tests and has basic functionality to get interactions by gene names. It sets a number of arguments by default (e.g., selfInteractionsExcluded = TRUE, includeInteractorInteractions = FALSE) - you can view the source of the function to see them.

Example usage is

library(rbiogrid)
set.access.key('XXXX')
get.interactions('PLK1') 
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Rajarshi Guha880

Thank you.

When I am trying to run the code, I get this error:

Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to webservice.thebiogrid.org port 80: Timed out

Do you know why this happens?

 

ADD REPLYlink written 5.0 years ago by Na Sed280

Not sure. The code works fine from here. Does http://webservice.thebiogrid.org/ resolve properly?

ADD REPLYlink written 5.0 years ago by Rajarshi Guha880
2
gravatar for Pierre Lindenbaum
5.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

yes, use the REST service http://wiki.thebiogrid.org/doku.php/biogridrest and the R methods to access the web http://www.math.ucla.edu/~anderson/rw1001/library/base/html/read.table.url.html

ADD COMMENTlink written 5.0 years ago by Pierre Lindenbaum126k
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