BUG: Metadata not updated after sample filtering #576
Description
What is the issue?
When filtering all samples with a specific metadata (e.g. when each sample is assigned a cell type in the metadata and all of those samples get filtered), the metadata is not updated to reflect the elimination of that specific metadata (e.g. all samples of cell type "Mast Cells" get filtered, but the entries in the metadata don't get filtered).
This becomes problematic in later analyses. I encountered this issue while doing ANOVA across all cell type groups. As there are no more data points because of the filtering, the anova couldn't produce any non-NaN p values.
How to reproduce the issue?
Manipulate any dataset so that all samples of a specific metadata group get filtered. This is as easy as just adding the sample manually to the protein data without any values and adding the new sample to the metadata with a unique value for a given metadata grouping. (e.g. instead of belonging to AD or CTR, the new sample belongs to TEST_GRP).
What is the expected behavior?
When filtering samples, the metadata should also be updated and returned from the step for access by future steps.