Check that cached artefacts still match the object's state

Returns TRUE when every requested artefact is fresh, otherwise a message describing the first problem. An artefact that is absent, or that predates provenance stamping, passes: unknown provenance is not the same as known bad.

Named in snake case rather than the checkXxx camel case of the other checkmate extensions in this package, because it validates object state rather than a params_*() list and sits alongside get_sc_cache_status().

Usage

check_sc_state(x, artefacts, modality = "rna")

Arguments

x

SingleCells, SingleCellsSubset, MetaCells or SingleCellsMultiModal class.

artefacts

Character vector. Artefacts to check, either an artefact kind ("pca", "knn", "snn", "magic") or an embedding name ("umap"). May be modality qualified ("adt:pca").

modality

String. Modality to resolve unqualified names against. One of c("rna", "adt", "atac", "wnn").

Value

TRUE if the check was successful, otherwise a string describing the failure.