Support for arbitratry design matrices and contrast vectors

[grst]

Is your feature request related to a problem? Please describe.
Most linear models support passing designs as design matrices and contrasts as contrast vectors. This is the "smallest common denominator" for specifying designs and it's useful

• for more complex designs and comparisons that aren't covered by a simple [column, baseline, treatment] triplet
• for writing wrapper functions (e.g. multi-condition-comparisions) that use PyDESeq2 as one of multiple backends and already deal with building model matrices and contrast vectors from more user-friendly input such as formulae.

Describe the solution you'd like

• DeSeqDataset should take a design matrix
• DeseqStats should take a contrast vector with one value per fitted coefficient, such as [0, -1, 1].

Additional context
discussed on the scverse hackathon in Cambridge

CC @const-ae @emdann

[BorisMuzellec]

Hi @grst @const-ae @emdann, is there a consensus regarding what would be most convenient? I'm assuming we want to use formulaic?

I won't have the bandwidth to implement this feature on my own in the next few weeks, but if anyone wants to give it a try, I'm happing to help them.

[grst]

I don't even think you'd need to deal with formulaic/patsy in PyDESeq2, at least initially. Either tool generates a design matrix (which advanced users could also create manually) which should be the input for PyDESeq2.

[const-ae]

I agree with Gregor that the easiest change might be to simply allow some way to provide a design matrix and then just skip the step build_design_matrix at https://github.com/owkin/PyDESeq2/blob/main/pydeseq2/dds.py#L249. Of course, longer term I think it would be great to save the user from converting data + formula to a design matrix and do it internally, but in the end it's just syntactic sugar :)

[jeandut]

The PR #181 is implementing the ability to give a design matrix directly however for now it needs to follow pydeseq2 naming conventions for further preprocessing namely the _vs_ syntax.

[jeandut]

Don't hesitate to play with the branch and give feedbacks on limitations.