loadTaxonomyDb {GenomeInfoDb} | R Documentation

## Return a data.frame that lists the known taxonomy IDs and their corresponding organisms.

### Description

NCBI maintains a collection of unique taxonomy IDs and pairs these with associated genus and species designations. This function returns the set of pre-processed values that we use to check that something is a valid Taxonomy ID (or organism).

### Usage

      loadTaxonomyDb()

### Value

A data frame with 1 row per genus/species designation and three columns. The 1st column is the taxonomy ID. The second columns is the genus and the third is the species name.

### Author(s)

Marc Carlson

### Examples

    ## get the data
    taxdb <- loadTaxonomyDb()
    tail(taxdb)
    ## which can then be searched etc.
    taxdb[grepl('yoelii', taxdb$species), ]

[Package GenomeInfoDb version 1.28.4 Index]