Contents
workspace$catalogs$genomeBuilds
Genome build catalog
Registry of the genome builds PolyGenius supports. Every other catalog
normalizes a user-supplied build string through this registry before using it
as a cache-identity parameter, a merge key or a manifest filter. Reached as
workspace$catalogs$genomeBuilds.
Details
The registry is static and in-memory — two rows, hg19 ("hg19/GRCh37") and
hg38 ("hg38/GRCh38"), built at construction. Nothing is downloaded, cached
or written, and there is no rule file behind it.
Matching is case- and whitespace-insensitive and by substring: the supplied
string is looked for inside both the key and the build column, so
"GRCh37" and "hg1" both resolve to hg19 while "hg" matches both rows
and aborts as ambiguous. key() and name() abort on an unmatched or
ambiguous string; label() never aborts, which is why the other catalogs'
view() methods use it per row.
Methods
Public methods
GenomeBuilds$new()GenomeBuilds$view()GenomeBuilds$key()GenomeBuilds$name()GenomeBuilds$label()GenomeBuilds$print()
Method new()
Build the two-row registry of supported genome builds.
Usage
GenomeBuilds$new()
Returns
A new GenomeBuilds object.
Method view()
Return the registry table.
Usage
GenomeBuilds$view()
Returns
A data.frame with one row per supported build and two character
columns: key ("hg19", "hg38") and build ("hg19/GRCh37",
"hg38/GRCh38").
Method key()
Resolve a build identifier to its canonical key.
Usage
GenomeBuilds$key(build)
Arguments
build — Character scalar. Build key or name, matched case- and
whitespace-insensitively as a substring of both registry columns.
Returns
Character scalar, "hg19" or "hg38". Aborts when build
matches no row or more than one.
Method name()
Resolve a build identifier to its canonical name.
Usage
GenomeBuilds$name(build)
Arguments
build — Character scalar. Build key or name, matched as for key().
Returns
Character scalar, "hg19/GRCh37" or "hg38/GRCh38". Aborts when
build matches no row or more than one.
Method label()
Return a display label for a build value without aborting on an unrecognized one.
Usage
GenomeBuilds$label(build, fallback = TRUE)
Arguments
build — Character scalar. Build key or name; NULL, a zero-length
value and NA all count as unresolved.
fallback — Logical scalar, default TRUE. When TRUE an unresolved
build is returned unchanged; when FALSE it becomes NA_character_.
Returns
Character scalar canonical build name, or the fallback above. Never aborts, even on an ambiguous string — the first match wins.
Method print()
Print the supported builds to the console.
Usage
GenomeBuilds$print(...)
Arguments
... — Unused. Present for print-method compatibility.
Returns
self, invisibly.
Examples
workspace$catalogs$genomeBuilds$view()
workspace$catalogs$genomeBuilds$key("GRCh38")
workspace$catalogs$genomeBuilds$label("hg99")See Also
Other catalogs:
LDblocks,
LDs,
LiftoverChains,
ReferencePanels,
VariantSpaces,
workspace_catalogs