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Add extra covariate support to combat. #618

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merged 4 commits into from Apr 29, 2019

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@gokceneraslan
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commented Apr 24, 2019

It's convenient to be able to specify multiple variables in combat in the R package. So I added the support for extra covariates (categorical or numeric) and converted some methods to private. There are tests for the new covariate option and also the private _design_matrix function now.

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commented Apr 26, 2019

This is great! 👍

Can you also update docs/release_notes.rst and then simply merge?

@gokceneraslan gokceneraslan force-pushed the gokceneraslan:combat-multivariable branch from 2c9772c to 149a5bf Apr 29, 2019

@gokceneraslan gokceneraslan force-pushed the gokceneraslan:combat-multivariable branch from 149a5bf to 4e81246 Apr 29, 2019

@gokceneraslan gokceneraslan merged commit 9b522f5 into theislab:master Apr 29, 2019

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@@ -13,6 +13,7 @@ On master :small:`April 27, 2019`
Bug fixes:

- :func:`~scanpy.tl.rank_genes_groups` t-test implementation doesn't return NaN when variance is 0, also changed to scipy's implementation, see `PR <https://github.com/theislab/scanpy/pull/621>`__ :smaller:`thanks to I Virshup`
- :func:`~scanpy.pp.combat` ComBat function now supports additional covariates which may include adjustment variables or biological condition, see `PR <https://github.com/theislab/scanpy/pull/618>`__ :smaller:`thanks to G Eraslan`

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falexwolf Apr 29, 2019

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Great, thank you!

@gokceneraslan gokceneraslan deleted the gokceneraslan:combat-multivariable branch Aug 21, 2019

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