Using a count matrix with NA values for GSEApy

zqfang / GSEApy

Gene Set Enrichment Analysis in Python

http://gseapy.rtfd.io/

BSD 3-Clause "New" or "Revised" License

560 stars 117 forks source link

Using a count matrix with NA values for GSEApy #256

Open LeilyR opened 7 months ago

LeilyR commented 7 months ago

Hi, I would like to use gsea function on a count matrix with NA. This is allowed by GSEA itself but I seem to not be able to use your tool when I have missing values. Do you have an option to ignore missing values, the way GSEA does. Thanks!

zqfang commented 7 months ago

I'm sorry, so far NaN is allowed in the input data (this is because of the rust backend). in your count matrix case, you can fill NA with 0.