AnnDbPkg-maker: Create an SQLite-based annotation package

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

Create an SQLite-based annotation package

Description

Create an SQLite-based annotation package from an SQLite file.

Usage

  makeAnnDbPkg(x, dbfile, dest_dir=".", no.man=FALSE, ...)
  loadAnnDbPkgIndex(file)

Arguments

x	A AnnDbPkgSeed object, a list, a string or a regular expression.
dbfile	The path to the SQLite containing the annotation data for the package to build.
dest_dir	The directory where the package will be created.
file	The path to a DCF file containing the list of annotation packages to build.
no.man	If TRUE then no man page is included in the package.
...	Extra args used for extra filtering.

See Also

AnnDbPkg-checker

Examples

  ## With a "AnnDbPkgSeed" object:
  seed <- new("AnnDbPkgSeed",
      Package="hgu133a2.db",
      Version="0.0.99",
      PkgTemplate="HUMANCHIP.DB",
      AnnObjPrefix="hgu133a2"
  )
  if (FALSE)
      makeAnnDbPkg(seed, "path/to/hgu133a2.sqlite")

  ## With package names:
  ## (Note that in this case makeAnnDbPkg() will use the package descriptions
  ## found in the master index file ANNDBPKG-INDEX.TXT located in the
  ## AnnotationDbi package.)
  if (FALSE)
      makeAnnDbPkg(c("hgu95av2.db", "hgu133a2.db"))

  ## A character vector of length 1 is treated as a regular expression:
  if (FALSE)
      makeAnnDbPkg("hgu.*")
  ## To make all the packages described in the master index:
  if (FALSE)
      makeAnnDbPkg("")
  ## Extra args can be used to narrow down the roaster of packages to make:
  if (FALSE) {
      makeAnnDbPkg("", PkgTemplate="HUMANCHIP.DB", manufacturer="Affymetrix")
      makeAnnDbPkg(".*[3k]\\.db", species=c("Mouse", "Rat"))
  }

  ## The master index file ANNDBPKG-INDEX.TXT can be loaded with:
  loadAnnDbPkgIndex()

Bioconductor/AnnotationForge documentation built on Oct. 29, 2023, 4:13 p.m.