workspace$catalogs$LDs

Read-only inventory of the built LD references available to PolyGenius. Reached as workspace$catalogs$LDs. These are LD storage artifacts — matrices and correlation references — not the block-boundary BED files of LDblocks.

Unlike the other catalogs this one is a view, not a resolvable resource type: it has no get(), no add(), no remove() and no rule file, so nothing it lists can be downloaded or built through it. view() unions whatever is already cached under the three LD storage types (ld.bigsnpr, ld.blocks, ld.gctb) with the read-only manifest shipped as inst/extdata/manifest.LDs.csv. Rows are keyed by the tuple reference.panel + build + method + measure + phased + ld.window + ld.window.kb + ld.window.r2.

Availability reads differently here than elsewhere: "registered" means declared in the manifest, not fetchable. The shipped manifest has zero data rows, so today view() returns cached references only. The producers are generate's LD-build rules, not this catalog.

Public methods

• LDs$new()
• LDs$view()
• LDs$print()

Method new()

Read the LD manifest and build the catalog.

Usage

LDs$new(manifest.path = NULL)

Arguments

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

Returns

A new LDs object. Aborts when the manifest file is absent, or is missing any of the columns name, reference.panel, build, method, measure, phased, ld.window, ld.window.kb, ld.window.r2, path, provenance, n.variants, description.

Method view()

List the LD references that are cached locally or declared in the manifest, optionally filtered.

Usage

LDs$view(name = NULL, reference.panel = NULL, build = NULL, method = NULL)

Arguments

name — Character vector of LD reference names, or NULL (default) to match any name.

reference.panel — Character vector of panel names, or NULL (default) to match any panel.

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

method — Character vector of LD methods, or NULL (default) to match any method.

Returns

A data.frame with columns name, reference.panel, build (as a display label from genomeBuilds$label()), method, measure, phased, ld.window, ld.window.kb, ld.window.r2, id (cache id, NA when not cached), path, provenance, n.variants, description, available.local, registered and availability (one of "here + registered", "here", "registered", "unavailable"). Reads the cache index; nothing is downloaded or built.

Method print()

Print the LD reference inventory, one line per entry, marking cached entries against manifest-only ones.

Usage

LDs$print(...)

Arguments

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

Returns

self, invisibly.

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