BUG update genewise dispersions and fitted dispersions of refitted genes

owkin / PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

https://pydeseq2.readthedocs.io/en/latest/

MIT License

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BUG update genewise dispersions and fitted dispersions of refitted genes #274

Closed BorisMuzellec closed 6 months ago

BorisMuzellec commented 6 months ago

What does your PR implement? Be specific.

Currently, when outlier genes are refitted, only "_normed_means", "LFC" and "dispersions" are updated in the fields of the DeseqDataSet, but not "genewise_dispersions" and "fitted_dispersions".

This has limited or no impact on the remainder of the code, but interferes with visualisation (e.g. with plot_dispersions().

This PR fixes this by also updating "genewise_dispersions" and "fitted_dispersions".

Example

Before:

After:

umarteauowkin commented 6 months ago

LGTM, thanks @BorisMuzellec