workspace$catalogs$referencePanels

Inventory of the reference panels available to PolyGenius, and the entry point that resolves one into the workspace cache. Reached as workspace$catalogs$referencePanels.

view() and get() see the union of two sources: the read-only manifest shipped as inst/extdata/manifest.referencePanels.csv, and whatever is already cached under <workspace$config$root>/reference.panel/. Rows are keyed by name + build + format, and a cached row's own fields win over the manifest's. add() and remove() touch the cache only; the manifest is never written.

A panel that is not directly downloadable at the requested build and format is derived — downloaded at its native build/format, then converted, lifted over, or restricted to a variant space — and every step is cached as a resource of its own. get() is therefore idempotent: a repeated call for the same panel reads the cache and downloads nothing.

Public methods

• ReferencePanels$new()
• ReferencePanels$view()
• ReferencePanels$get()
• ReferencePanels$add()
• ReferencePanels$remove()
• ReferencePanels$key()
• ReferencePanels$assert.unrestricted()
• ReferencePanels$print()

Method new()

Read the reference-panel manifest and build the catalog.

Usage

ReferencePanels$new(manifest.path = NULL)

Arguments

manifest.path — Character scalar path to a manifest CSV, or NULL (default). NULL reads inst/extdata/manifest.referencePanels.csv from the installed package.

Returns

A new ReferencePanels object. Aborts when the manifest file is absent, or is missing any of the columns name, build, format, files, description, url, sha256, source.reference.panel, variant.space.

Method view()

List every panel that is cached locally or downloadable.

Usage

ReferencePanels$view()

Returns

A data.frame, one row per name + build + format, sorted by those three columns, with columns key, name, build (as a display label from genomeBuilds$label()), format, id (cache id, NA when not cached), files, description, path, url, sha256, source.reference.panel, variant.space, available.local, available.download, downloadable and availability. sha256 always comes from the manifest, never from a cache row, because the stored panel is the unpacked and tidied fileset and not the .tar.gz the checksum measured. Reads the cache index; nothing is downloaded.

Method get()

Resolve one reference panel, materializing it into the cache when it is not there yet.

Usage

ReferencePanels$get(
  name,
  build = NULL,
  format = NULL,
  variant.space = NULL,
  .execute = TRUE,
  .status = polygenius.option.execution.status()
)

Arguments

name — Character scalar. Panel display name or internal key.

build — Character scalar build key/name, or NULL (default). NULL accepts whichever build the inventory match supplies.

format — One of "pfile", "bfile", "vcf", or NULL (default). NULL accepts whichever format the inventory match supplies.

variant.space — Character scalar variant-space name, or NULL (default). When supplied, resolves the panel restricted to that variant space, defaulting the target format to "pfile"; name must then be an unrestricted panel and build must be given.

.execute — Logical scalar, default TRUE. When TRUE, run the producing rules — downloading, converting, lifting over or restricting as needed — so the panel is present in the cache before returning.

.status — One of "auto", "yes", "no"; default polygenius.option.execution.status(), which is "yes". Execution-status display mode for this call.

Returns

When .execute = TRUE, a GenotypeSource pointing at the cached panel. When .execute = FALSE, a ResourceSpecSet describing what would be produced, with nothing downloaded. Aborts when name is unknown and build and format are not both given, when the filters match several inventory rows and build and format are not both given, and — with variant.space — when build is missing or name is already restricted.

Method add()

Register local genotype filesets as cached reference panels.

Usage

ReferencePanels$add(..., overwrite = FALSE)

Arguments

... — One or more GenotypeSource objects. A named argument uses its name as the panel name; an unnamed one uses GenotypeSource$name.

overwrite — Logical scalar, default FALSE. When FALSE, an input whose name + build + format is already cached aborts the whole call.

Returns

Invisibly, a ResourceSpec when one panel was added, otherwise a list of them. Each panel is merged into a single fileset, tidied to its own format with standardized variant IDs and chromosome format 26, and written under <workspace$config$root>/reference.panel/<id>/ with a store index entry. Aborts when no object is given, when an entry is not a GenotypeSource, when a panel name is empty, or when two inputs share one name + build + format.

Method remove()

Delete cached reference panels matching the given filters.

Usage

ReferencePanels$remove(name = NULL, build = NULL, format = NULL)

Arguments

name — Character scalar panel name or key, or NULL (default) to match any name.

build — Character scalar build key/name, or NULL (default) to match any build. An unrecognized build string aborts.

format — Character scalar format, or NULL (default) to match any format.

Returns

NULL, invisibly. Deletes each matching resource directory under <workspace$config$root>/reference.panel/ and its store index rows, and reports the count. Called with no arguments it removes every cached reference panel. The manifest is untouched, so a removed downloadable panel still appears in view() and get() re-downloads it.

Method key()

Resolve a panel display name to its internal key.

Usage

ReferencePanels$key(name)

Arguments

name — Character scalar. Panel display name or internal key.

Returns

Character scalar internal key. Aborts when name matches no inventory row and is not a well-formed restricted-panel key.

Method assert.unrestricted()

Assert that a panel is not already restricted to a variant space, the precondition for restricting it.

Usage

ReferencePanels$assert.unrestricted(name)

Arguments

name — Character scalar. Panel display name or internal key.

Returns

TRUE, invisibly. Aborts when name parses as a restricted-panel key or its inventory row carries a source.reference.panel.

Method print()

Print the panel inventory, one line per entry, marking cached entries against downloadable ones.

Usage

ReferencePanels$print(...)

Arguments

... — Unused. Present for print-method compatibility.

Returns

self, invisibly.

Other catalogs: GenomeBuilds, LDblocks, LDs, LiftoverChains, VariantSpaces, workspace_catalogs