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sidmall / PDSclassifier

GNU General Public License v3.0
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Error with running calculateSMI function #2

Closed ttszen closed 4 months ago

ttszen commented 4 months ago

Hello! Thank you very much for this useful tool and congratulations on the recent publication of your paper!

I was trying to run the calculateSMI function on some scRNA-seq data. I ran into the following error.

Error: 'enrichIt' is not an exported object from 'namespace:escape' and I was using version 1.12.0 of the escape R package.

I updated escape to the latest version of R and found that the enrichIt function has now been updated to escape.matrix() based here: https://github.com/ncborcherding/escape/blob/master/NEWS.md.

I was wondering if the PDSclassifier package would be updated to reflect this change?

It'd be great to get your thoughts on this and happy to discuss further.

sidmall commented 4 months ago

Hi @ttszen,

Thank you for notifying us.

Yes, we will look into this matter on the recent update of escape R package, and plan on modifying the calculateSMI function in PDSclassifier accordingly in the near future.

But, in case you require to calculate SMI right away, I would suggest you to look up the 'Method' section in now published article: https://www.nature.com/articles/s41588-024-01654-5 which details how to calculate SMI.

Thanks again.

ttszen commented 4 months ago

Hi @sidmall, thank you for getting back to me. Sure, that sounds good. I've been able to run the calculateSMI function by downgrading my R and bioconductor versions so I have a solution for now.

Looking forward to future updates!