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

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

biogrid gene interaction network r
• 6,179 views • link
updated by Ram Ram • written by Na Sed Na Sed

2 answers

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')
• 0 views • link
updated by Ram Ram • written by Rajarshi Guha Rajarshi Guha

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?

• 0 views • link
updated by Ram Ram • written by Na Sed Na Sed

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

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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