search

owkin / PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
https://pydeseq2.readthedocs.io/en/latest/
MIT License
573 stars 60 forks source link

MAINT cast counts to int when initialising a DeseqDataSet from anndata #299

Closed BorisMuzellec closed 2 months ago

BorisMuzellec commented 2 months ago

Reference Issue or PRs

Related to #291

What does your PR implement? Be specific.

When we create a DeseqDataSet from a counts and a metadata dataframes, counts are automatically cast to int, but not when we create one from a pre-existing anndata object.

This may apparently cause bugs (cf. #291).

This PR fixes this by casting anndata counts to int by default.