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)

Arguments

version

What is the version number for this package?

maintainer

Who is the package maintainer? (must include email to be valid)

author

Who is the creator of this package?

outputDir

A path where the package source should be assembled.

tax_id

The Taxonomy ID that represents your organism. (NCBI has a nice online browser for finding the one you need)

genus

Single string indicating the genus.

species

Single string indicating the species.

NCBIFilesDir

If you want the files to be saved locally that were used to make your DB, then specify a directory here. Otherwise leave this NULL. This argument is mostly useful for troubleshooting since many of the files are large. Most users should ignore it.

databaseOnly

Only generate a DB without a package (TRUE or FALSE)

useDeprecatedStyle

For legacy support in those cases where it will actually work. Should we use the older database and package style (with bimaps)? (TRUE or FALSE) Also: this can't work with unsupported organisms

Value

annotation package.

Examples

Run this code


## 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)

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