genomes (version 2.16.0)

genomes-update: Genome table updates

Description

Generic function for updating genome tables.

Usage

"update"(object, ...)

Arguments

object

a genomes data frame to update

...

additional arguments are currently ignored

Value

Returns the updated genome table and a count of the number of new IDs added and old IDs removed. Old IDs are typically assembly genomes in NCBI tables that have been released as a single complete genome.

Details

update will retrieve the new genome table using the update string in attr(object, 'update'). The new table will replace the existing version, but not permanently, since reloading the dataset using data will restore the older version. If you have write permission, one option is to use system.file to replace the data set (see the example below).

See Also

genomes-summary, genomes-plot

Examples

## Not run: data(proks)
## Not run: update(proks)

# to replace the data set permanently
x <- system.file("data", "proks.rda", package="genomes")
x
## Not run: save(proks, file=x)