workspace$catalogs$LDblocks

Inventory of approximately-independent LD block boundary sets (Berisa & Pickrell), keyed by population and genome build. Reached as workspace$catalogs$LDblocks. These are boundary BED files, not built LD matrices — for those see LDs.

view() and get() see the union of the read-only manifest shipped as inst/extdata/manifest.LDblocks.csv and whatever is already cached under <workspace$config$root>/ld.block.boundaries/. add() and remove() touch the cache only; the manifest is never written.

A set the manifest does not ship for a build can be derived by lifting the same population over from another build, and the derived set is cached under its own identity, so a repeated get() reads the cache and downloads nothing. The stored form is always the same, whichever door a set arrived through: a headerless tab-separated blocks.bed of chr/start/end, autosomes only, sorted, and a gapless per-chromosome partition.

Public methods

• LDblocks$new()
• LDblocks$view()
• LDblocks$get()
• LDblocks$add()
• LDblocks$remove()
• LDblocks$print()

Method new()

Read the LD block boundary manifest and build the catalog.

Usage

LDblocks$new(manifest.path = NULL)

Arguments

manifest.path — Character scalar path to a manifest CSV, or NULL (default). NULL reads inst/extdata/manifest.LDblocks.csv from the installed package. The CSV must carry population, build, url, sha256 and description columns.

Returns

A new LDblocks object. Aborts when the manifest file is absent or is missing any required column.

Method view()

List every block set that is cached locally or downloadable.

Usage

LDblocks$view()

Returns

A data.frame, one row per population + build, sorted by those two columns, with columns population, build (as a display label from genomeBuilds$label()), id (cache id, NA when not cached), path, url, sha256, description, available.local, downloadable and availability. sha256 always comes from the manifest, never from a cache row, because the stored file is the harmonized partition and not the published BED the checksum measured. Reads the cache index; nothing is downloaded.

Method get()

Resolve every block set matching the filters, materializing any that is not cached yet.

Usage

LDblocks$get(
  population = NULL,
  build = NULL,
  .execute = TRUE,
  .status = polygenius.option.execution.status()
)

Arguments

population — Character scalar population code (e.g. "EUR"), uppercased before matching, or NULL (default) to match any population.

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

.execute — Logical scalar, default TRUE. When TRUE, run the producing rules — downloading or lifting over as needed — so each matched set 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 and exactly one set matched, a named list with one element, path, the cached blocks.bed; when several matched, a list of such lists. When .execute = FALSE, a ResourceSpecSet, with nothing downloaded. Aborts when no inventory row matches the filters, or when the build string is unrecognized.

Method add()

Register a local block-boundary BED file as a cached set.

Usage

LDblocks$add(population, build, path, overwrite = FALSE)

Arguments

population — Character scalar population code (e.g. "EUR"), uppercased before use.

build — Character scalar build key/name.

path — Character scalar path to an existing BED file, plain or gzipped. A chr start stop header row and chr-prefixed names are both accepted.

overwrite — Logical scalar, default FALSE. When FALSE, an already cached population + build aborts the call.

Returns

A ResourceSpec, invisibly. Harmonizes the file — autosomes only, sorted, coerced to a gapless per-chromosome partition — and writes it as <workspace$config$root>/ld.block.boundaries/<id>/blocks.bed with a store index entry, the same identity and stored form a downloaded set gets. Aborts when path does not exist or is empty, when a row has fewer than three whitespace-separated fields, when no usable autosomal block survives, or when the result is not a non-overlapping partition.

Method remove()

Delete cached block-boundary sets matching the given filters.

Usage

LDblocks$remove(population = NULL, build = NULL)

Arguments

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

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

Returns

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

Method print()

Print the block-boundary inventory, one line per entry, marking cached entries against downloadable ones.

Usage

LDblocks$print(...)

Arguments

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

Returns

self, invisibly.

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