PyDESeq2
PyDESeq2 copied to clipboard
Support for arbitratry design matrices and contrast vectors
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