Entering edit mode
Hello,
Is there anyway to modify the get_interactions function from the stringdb package so that I can sort through the interactions I need and not have to work with the combined score?
Thanks!
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version 2.3.6
version 2.3.6
You can specify the score cut-off with score_threshold parameter, when initiating the string_db object.
I meant I want to filter out the interaction types to include only experimental and database. The combined score would include all the different types of interactions that I do not care about
The network won't be by default filtered by the experimental score, but you can obtain it if you use the link_data='detailed' parameter. This will include the evidence channels score in the table, which then you can use for filtering.
I'm running the current vignette which is still giving me "link_data the missing variable.
Sorry, for the confusion. Please make sure you are using the current (2.16.4) version of the package.
I am having a similar issue. However when I tried the solution that you suggested it did not work. Initializing a database with the exact syntax you gave gives the error link_data is not a field in class STRINGdb. I also searched through the documentation and it does not have a clear solution either.
I would also like to add that while combing through the source code for this package, I can see that link_data is indeed a variable that should be able to be added to this. So I am not exactly sure what is going on here. I may try rebuilding my environment with an older version of the package.
Indeed. If you see the "link_data" missing error, it means you have an older version of the package. The current vignette, which includes this variable should run without an issue.
Great thank you. I changed compilers and built the package from the tarball and it seems to be working now. Cheers