makeOrgPackageFromNCBI {AnnotationForge} | R Documentation

## 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)

[Package AnnotationForge version 1.34.1 Index]