AnnDbPkg-maker: Create an SQLite-based annotation package

Description Usage Arguments See Also Examples

Description

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

Usage

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  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

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  ## 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()

AnnotationForge documentation built on May 2, 2018, 3:19 a.m.