workspace\(catalogs\)variantSpaces

Variant Space Catalog

Description

Inventory and management utility for workspace variant-space resources.

Details

Inventory and management utility for named variant sets used to restrict reference panels and define default PCA/kinship variant spaces.

Use this catalog through workspace$catalogs$variantSpaces.

Methods

Public methods

Method new()

Initialize variant-space catalog.

Usage 
VariantSpaces$new(manifest.path = NULL)
Arguments
manifest.path

Optional custom manifest CSV path.

Method view()

View local and downloadable variant spaces.

Usage 
VariantSpaces$view()
Returns

data.frame inventory with availability flags.

Method get()

Resolve a variant-space resource.

Usage 
VariantSpaces$get(
  name,
  build = NULL,
  .execute = TRUE,
  .status = polygenius.option.execution.status()
)
Arguments
name

User-facing name or internal key.

build

Optional genome-build key/name filter.

.execute

Logical; when TRUE, trigger reactive execution.

.status

Optional execution-status mode override.

Returns

When .execute = TRUE, a resolved variant-space resource value. When .execute = FALSE, a ResourceSpecSet.

Method add()

Add a local variant-space file or table to the cache.

Usage 
VariantSpaces$add(name, build, variants, overwrite = FALSE)
Arguments
name

User-facing variant-space name.

build

Genome build.

variants

Data frame or file path readable by data.table::fread().

overwrite

Logical; overwrite an existing cached entry.

Returns

Invisible ResourceSpec.

Method remove()

Remove cached variant spaces matching optional filters.

Usage 
VariantSpaces$remove(name = NULL, build = NULL)
Arguments
name

Optional user-facing name or key.

build

Optional genome build.

Returns

Invisible NULL.

Method key()

Resolve a user-facing name or key into an internal key.

Usage 
VariantSpaces$key(name, build = NULL)
Arguments
name

User-facing name or key.

build

Optional genome build.

Returns

Internal key.

Method print()

Print variant-space inventory summary.

Usage 
VariantSpaces$print(...)
Arguments
…

Unused.