
makeOrganismPackage
is a method that generates a package
that will load an appropriate annotationOrganismDb
object that
will in turn point to existing annotation packages.
makeOrganismPackage (pkgname, graphData, organism, version, maintainer, author, destDir, license="Artistic-2.0")
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.
OrganismDb
## 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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