makeOrgPackageFromNCBI: Make an organism package from annotations available from...

In Bioconductor/AnnotationForge: Tools for building SQLite-based annotation data packages

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,
    ensemblVersion=NULL)

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.
ensemblVersion	Ensmbl version to use. When NULL, uses the current version.

Details

makeOrgPackageFromNCBI downloads multiple files and assembles a 33 GB database in NCBIFilesDir. The first time the function is run it may take well 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).

The files that are downloaded from NCBI may take longer to download than the default timeout permits. We encourage users to set a options(timeout=xxx) to encourage the files to finish downloading. Adjust the timelimit according to download speed and capacity.

Depending on the organism, the database file could reach up to 49 G. You will need ~62G free for downloading files and creating the largest database as of February 2022.

Some orgDbs are already provided through AnnotationHub. See package AnnotationHub::AnnotationHub

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 <[e-mail]>",
                       maintainer = "Some One <[e-mail]>",
                       outputDir = ".",
                       tax_id = "59729",
                       genus = "Taeniopygia",
                       species = "guttata")


## End(Not run)

Bioconductor/AnnotationForge documentation built on Oct. 29, 2023, 4:13 p.m.