NEWS

MultiAssaySpatialExperiment 0.99.2

Added \value sections (roxygen @return) to the MultiAssaySpatialExperiment class, combine, subset, and SpatialExperiment-coercion man pages, and to SpatialLayerList-class, documenting the values returned by the constructors, accessors, replacement, coercion, combining, and subsetting methods. Resolves the R CMD BiocCheck "missing \value" WARNING.

readMERSCOPEMASE() and readCosMxMASE() now have runnable examples backed by minimal mock output directories bundled under inst/extdata/ (merscope_mock/, cosmx_mock/; generated by inst/scripts/make-example-mocks.R). This raises the share of exported-object man pages with runnable examples above the 80% BiocCheck threshold, resolving the R CMD BiocCheck ERROR.

Reconciled the vignettes into a numbered, user-first set:
- 1. Introduction to MultiAssaySpatialExperiment --- overview, anatomy, construction, accessors, subsetting, spatial operations, coercion, and a compact quick-reference table.
- 2. Working with MultiAssaySpatialExperiment --- construction patterns, subsetting, spatial annotation and aggregation, and labels <-> shapes.
- 3. MultiAssaySpatialExperiment use cases --- platform readers (Xenium, Visium, Visium HD, CosMx, MERSCOPE) and real-world spatial workflows.
Removed the Cheatsheet vignette (its chunks were globally unevaluated, which BiocCheck flags); its quick-reference content is now a table in the Introduction.
Applied Bioconductor vignette conventions: numbered VignetteIndexEntry, BiocStyle::doc_date() compiled dates, and structured author metadata.