AnnotationForge: makeOrgPackageFromNCBI – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

makeOrgPackageFromNCBI

Make an organism package from annotations available from NCBI.

Description

The makeOrgPackageFromNCBI function allows the user to make an organism package from NCBI annotations available from the NCBI.

Usage

makeOrgPackageFromNCBI(
    version=,
    maintainer,
    author,
    outputDir=getwd(),
    tax_id,
    genus=NULL,
    species=NULL,
    NCBIFilesDir=getwd(),
    databaseOnly=FALSE,
    useDeprecatedStyle=FALSE,
    rebuildCache=TRUE,
    verbose=TRUE)

Arguments

`version`	Package version in 'x.y.z' format.
`maintainer`	Package maintainer followed by email
`author`	Creator of package.
`outputDir`	Path where the package source should be assembled.
`tax_id`	The Taxonomy ID that represents the organism.
`genus`	Single string indicating the genus.
`species`	Single string indicating the species.
`NCBIFilesDir`	When a path is given, the files used to create the DB are saved locally.
`databaseOnly`	When TRUE, a DB is created without the package infrastructure. Used for OrgDb packages hosted on AnnotationHub.
`useDeprecatedStyle`	Legacy support for older package style with bimaps.
`rebuildCache`	When TRUE, the files used to create the DB are refreshed (i.e., re-downloaded) if the timestamp is greater than 24 hours old. When FALSE, the temporary NCBI.sqlite DB and final package are re-generated from local files in `outputDir`. Used internally and for testing.
`verbose`	When TRUE, status messages are printed.

Details

makeOrgPackageFromNCBI downloads multiple files and assembles a 12 GB database in NCBIFilesDir. The first time the function is run it may take over an hour; subsequent calls reuse files from the cache and are much faster. The default behavior of makeOrgPackageFromNCBI attempts to refresh the cached files each day (suppress with rebuildCache = FALSE).

Value

Nothing returned to the R session. Just creates an organism annotation package.

Author(s)

M. Carlson

Examples

## Not run: 
## Makes an organism package for Zebra Finch from NCBI:

makeOrgPackageFromNCBI(version = "0.1",
                       author = "Some One <so@someplace.org>",
                       maintainer = "Some One <so@someplace.org>",
                       outputDir = ".",
                       tax_id = "59729",
                       genus = "Taeniopygia",
                       species = "guttata")


## End(Not run)

AnnotationForge

Tools for building SQLite-based annotation data packages

v1.32.0

Artistic-2.0

Authors

Marc Carlson, Hervé Pagès

Initial release