get_pseudobulk() gained as_SummarizedExperiment to optionally return a SummarizedExperiment. Coercion restores feature rownames, which are otherwise dropped by as(x, "SummarizedExperiment").
Tests. Added a test ensuring feature rownames are preserved when as_SummarizedExperiment = TRUE.
Consistent features handling across retrieval functions. get_pseudobulk(), get_single_cell_experiment(), and get_metacell() now drop experiments/samples that do not contain all requested features and align rows to the requested feature set before merging. A warning indicates how many experiments were dropped.
Stabilised feature subsetting during merge to avoid index/subscript errors and ensure identical row order across experiments prior to cbind().
Qualified functional calls (e.g., purrr::map_lgl) to avoid missing import issues.
Documentation updates. Clarified the features parameter docs for all three functions to describe the drop-and-align behavior; regenerated help files.
Tests. Added a test verifying pseudobulk subsetting to the specific feature ENSG00000065485.
Added a NEWS file to track changes to the package.