-1
$\begingroup$

I need to retreive a large dataset from String-db. I 'm newbie in R so even with the documentation , I could not get the dataset fron String How do I do to retreive a network from String 2k to 3k proteins what are the functions to use for such matter ?

$\endgroup$
1
  • $\begingroup$ I think this question belongs to Stack Overflow $\endgroup$ – Bilal May 23 '17 at 20:04
0
$\begingroup$

String uses REST API, although the link to the help page for that results in a blank page instead (contact the authors!). In general, I would use the API. Alternatively, just download the database locally, they have a quite neat collection ready to be downloaded

$\endgroup$
9
  • $\begingroup$ If I donwload it locally , I can retreive 200k proteins ? and download the network I need right ? $\endgroup$ – A M May 24 '17 at 14:09
  • $\begingroup$ Correct. Check the download page, they have different "packets" download the one you are interested in. $\endgroup$ – alec_djinn May 24 '17 at 14:14
  • $\begingroup$ Okay I'm downloading the first packet in the interaction data section for homosapien. What I don't get is that how am I going to use it ? how would I know the proteins or the specific network for cacaner ? $\endgroup$ – A M May 24 '17 at 14:30
  • $\begingroup$ It has 11353057 interaction , I have no Idea how to get only cancer network ? $\endgroup$ – A M May 24 '17 at 15:04
  • $\begingroup$ You need to have list of protein you are interested in. There is no shuch a thing like a "cancer network" you may find different databases online, like the COSMIC, that lists genes found to be linked with cancer. You can start there. But this goes beyond your question. $\endgroup$ – alec_djinn May 25 '17 at 10:47

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.