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!
Traffic: 615 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
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