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 ?
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$\begingroup$ I think this question belongs to Stack Overflow $\endgroup$– BilalMay 23, 2017 at 20:04
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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
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$\begingroup$ If I donwload it locally , I can retreive 200k proteins ? and download the network I need right ? $\endgroup$– A MMay 24, 2017 at 14:09
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$\begingroup$ Correct. Check the download page, they have different "packets" download the one you are interested in. $\endgroup$ May 24, 2017 at 14:14
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$\begingroup$ 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 MMay 24, 2017 at 14:30
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$\begingroup$ It has 11353057 interaction , I have no Idea how to get only cancer network ? $\endgroup$– A MMay 24, 2017 at 15:04
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$\begingroup$ 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. $\endgroup$ May 25, 2017 at 10:47