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martinjzhang / scDRS

Single-cell disease relevance score (scDRS)
https://martinjzhang.github.io/scDRS/
MIT License
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Adjusting for donor effects #48

Closed Ararder closed 1 year ago

Ararder commented 1 year ago

Hi! Thanks very much for the great work behind scDRS. It's great to use.

I was wondering if you have thoughts on how to adjust for potential donor effects? Is it best to add one-hot encodings for each donor, or provide one column with a different value for each donor?.

martinjzhang commented 1 year ago

Hi @Ararder

Thank you for the question. You can use the scdrs compute-score --cov-file function to adjust for donor effects. To do so, you can add one-hot encoding of each donor (all but one) to the .cov file. For example, if there are 3 donors, the .cov file should contain 3 binary variables: const (all 1), donor1, and donor2.