AnnotationForge (version 1.14.2)

makeOrgPackageFromNCBI: Making 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.

Value

annotation package.

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).

Examples

## Not run: 
# ## Makes an organism package for Zebra Finch from NCBI:
# 
# makeOrgPackageFromNCBI(version = "0.1",
#                        author = "Some One <[e-mail]>",
#                        maintainer = "Some One <[e-mail]>",
#                        outputDir = ".",
#                        tax_id = "59729",
#                        genus = "Taeniopygia",
#                        species = "guttata")
# 
# ## End(Not run)