Can't create STRINGdb v11 object using STRINGdb packages methods
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Moosa • 0
@moosa-20888
Last seen 2.4 years ago

Hello. when I try to create a STRINGdb object, using the following code:

> library(STRINGdb)
> string_db = STRINGdb$new(version = "11", species=9606, score_threshold=700, input_directory="stringdbdata/")

I get this error:

ERROR: The version  11 is not valid. 
Please use one of the following versions:
9_05, 9_1, 10Error in .Object$initialize(...) :

As I understand, version 11 is out since January, and it is accessible from here. Does it mean that STRINGdb's R interface is not compatible with version 11 or am I doing something wrong with my code?

My other question is that, suppose I downloaded all the required files manually, is there a method to load them into a STRINGdb object? I've read the package's vignette and documentations, but since I'm a beginner at R, I couldn't find an answer. Thank you for your time.

stringdb • 593 views
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Dear Moosa,

Indeed STRING 11 is not available through the R package. The APIs are not compatible with the latest release and we are working on the new version at the moment.

We don't have the exact date when it'll be released. Sorry for the inconvenience.

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Dear Damian, Thank you for your help, I'm sorry to bother you with my novice questions, can I download and parse the Interaction data and another required file manually, and then load it into a STRINGdb object for further analysis?

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Dear Moosa, it won't work, as STRINGv11 and STRINGv10 use different protein name-space (and different proteome themselves) If you are interested in network and/or enrichment analysis, please refer to our API. It covers the main functionality of our R package.

https://string-db.org/cgi/help.pl?subpage=api

Again, sorry for the inconvenience.

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Dear Damian.

I appreciate your great help and informative answers. your API is truly amazing. My sincere thanks and respect to you again for your kind answers here and for the great effort you have put into STRINGdb.

best regard. :)

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