makeOrganismPackage: Making OrganismDb packages from annotation packages.

Description

makeOrganismPackage is a method that generates a package that will load an appropriate annotationOrganismDb object that will in turn point to existing annotation packages.

Usage

makeOrganismPackage (pkgname, graphData, organism, version, maintainer, author, destDir, license="Artistic-2.0")

Arguments

pkgname

What is the desired package name. Traditionally, this should be the genus and species separated by a ".". So as an example, "Homo.sapiens" would be the package name for human

graphData

A list of short character vectors. Each character vector in the list is exactly two elements long and represents a join relationship between two packages. The names of these character vectors are the package names and the values are the foreign keys that should be used to connect each package. All foreign keys must be values that can be returned by the columns method for each package in question, and obviously they also must be the same kind of identifier as well.

organism

The name of the organism this package represents

version

What is the version number for this package?

maintainer

Who is the package maintainer? (must include email to be valid)

author

Who is the creator of this package?

destDir

A path where the package source should be assembled.

license

What is the license (and it's version)

Value

OrganismDb object.

Details

The purpose of this method is to create a special package that will depend on existing annotation packages and which will load a special annotationOrganismDb object that will allow proper dispatch of special select methods. These methods will allow the user to easily query across multiple annotation resources via information contained by the annotationOrganismDb object. Because the end result will be a package that treats all the data mapped together as a single source, the user is encouraged to take extra care to ensure that the different packages used are from the same build etc.

Examples

Run this code

## set up the list with the relevant relationships:
gd <- list(join1 = c(GO.db="GOID", org.Hs.eg.db="GO"),
           join2 = c(org.Hs.eg.db="ENTREZID",
                     TxDb.Hsapiens.UCSC.hg19.knownGene="GENEID"))

## sets up a temporary directory for this example
## (users won't need to do this step)
destination <- tempfile()
dir.create(destination)

## makes an Organism package for human called Homo.sapiens
if(interactive()){
  makeOrganismPackage(pkgname = "Homo.sapiens",
   graphData = gd,
   organism = "Homo sapiens",
   version = "1.0.0",
   maintainer = "Bioconductor Package Maintainer <maintainer@bioconductor.org>",
   author = "Bioconductor Core Team",
   destDir = destination,
   license = "Artistic-2.0")
}

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