R in KNIME with Molecular fingerprints

Hi All,

I am trying to build QSPR models in KNIME using R. I want to use the molecular fingerprints as  dependent variables. When I use it, "R Learner" doesn't recognise the fingerprint column and results in an error.

Can someone please help me in this aspect? Do I have to convert the "bit" format fingerprint into R-readable format? If so, how and which?

Your inputs will be higly appreciated.

Pankaj

Hi Pankaj,

Have a look at the attached workflow and let me know if it helps at all.  One branch shows how to use the native Bayes fingerprint learner and predictor, while the other relies on the Erl Wood fingerprint expander to create a set of regular int columns that you can use to  train your model.

Regards,

Aaron

Thanks Aaron,

This worked very well, as required. 

Regards

Pankaj

wow..thanks for sharing this to us.. it could be helpful to the people..

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