ENH multi-level design support#101

Merged

BorisMuzellec merged 12 commits intomainfrom

contrast_vector

Mar 22, 2023

Commits on Mar 17, 2023

feat: build design matrices for n-level multi-factor designs
Boris MUZELLEC
committed
refactor: remove the possibility to choose a reference level at DeseqDataSet instantiation, this is to be done using contrasts
Boris MUZELLEC
committed
feat: adapt DeseqStats contrast and LFC to n-level multifactor
Boris MUZELLEC
committed
fix: type hinting
Boris MUZELLEC
committed

Commits on Mar 20, 2023

feat: implement n-level multifactor wald tests, based on contrast vectors
Boris MUZELLEC
committed
refactor: factor-out contrast building in a dedicated private method
Boris MUZELLEC
committed
feat: allow user to specify which variable and level will be tested when initializing a DeseqDataSet (prepares LFCshrink)
Boris MUZELLEC
committed
feat: adapt lfc shrinkage to n-level factors
Boris MUZELLEC
committed
docs: add coeff argument to lfc_shrink
Boris MUZELLEC
committed

Commits on Mar 22, 2023

fix: typo

BorisMuzellec
and
maikia
authored
test: test that DeseqStats throws errors when provided an invalid contrast
Boris MUZELLEC
committed
test: check that a KeyError is thrown when shrinking an unexisting coeff
Boris MUZELLEC
committed