available.db0pkgs: available.db0pkgs

In Bioconductor/AnnotationForge: Tools for building SQLite-based annotation data packages

available.db0pkgs

Description

Get the list of intermediate annotation data packages (.db0 data packages) that are currently available on the Bioconductor repositories for your version of R/Bioconductor.

Or get a list of schemas supported by AnnotationDbi.

Usage

  available.db0pkgs()
  available.dbschemas()
  available.chipdbschemas()

Details

The SQLForge code uses a series of intermediate database packages that are necessary to build updated custom annotation packages. These packages must be installed or updated if you want to make a custom annotation package for a particular organism. These special intermediate packages contain the latest freeze of the data needed to build custom annotation data packages and are easily identified by the fact that they end with the special ".db0" suffix. This function will list all such packages that are available for a specific version of bioconductor.

The available.dbschemas() and available.chipdbschemas() functions allow you to get a list of the schema names that are available similar to how you can list the available ".db0" packages by using available.db0pkgs(). This list of shemas is useful (for example) when you want to build a new package and need to know the name of the schema you want to use.

Value

A character vector containing the names of the available ".db0" data packages. Or a a character vector listing the names of the available schemas.

Author(s)

Hervé Pagès and Marc Carlson

Examples

  # Get the list of BSgenome data packages currently available:
  available.db0pkgs()

  ## Not run: 
    # Make your choice and install like this:
    library(BiocManager)
    install("human.db0")
  
## End(Not run)

  # Get the list of chip DB schemas:
  available.chipdbschemas()

  # Get the list of ALL DB schemas:
  available.dbschemas()

Bioconductor/AnnotationForge documentation built on Nov. 2, 2024, 6:30 a.m.