Update a VISTA object to the current metadata schema

Brings a VISTA object created by an older version of the package up to the current metadata layout. Missing metadata keys are back-filled with their documented defaults, the schema tag is stamped to the running version, and the migration is recorded in metadata(x)$provenance$updates.

Usage

# S4 method for class 'VISTA'
updateObject(object, ..., verbose = FALSE)

Arguments

object

A VISTA object.

...

Passed to other methods (unused).

verbose

Logical; report what was migrated.

Value

A VISTA object stamped with the current schema version.

Details

Some content cannot be recovered by migration. In particular, objects built before VISTA 1.2.0 did not retain raw counts, and normalized counts are not invertible – counts() on such an object reports that a rebuild is required rather than inventing values.

Objects carrying a newer schema than the running package are left untouched and reported by validate_vista() as an issue, because newer metadata may carry semantics this version would misread.

Examples

v <- example_vista()

# Simulate an object written by an older release.
S4Vectors::metadata(v)$vista_schema_version <- "0.9.0"
v2 <- BiocGenerics::updateObject(v)
S4Vectors::metadata(v2)$vista_schema_version
#> [1] "1.1.0"