Species and taxonomy ID look up tables

Description

This package contains three mapping objects:

• speciesMap: A data frame with columns ‘tax_id’, ‘genus’, and ‘species’. Used to retrieve taxonomy ID by species and returns list of available species.

• validTaxIds: An integer vector of valid taxonomy IDs created from speciesMap. Used internally for quick taxonomy ID look ups.

• specData: A data frame with columns ‘taxon’ and ‘species’. Used internally to retrieve species by taxonomy ID.

Usage

data(speciesMap)
data(validTaxIds)
data(specData)

Details

Scripts to generate these files are in GenomeInfoDbData/inst/scripts. All originate from the taxdummp download at ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz.

Author(s)

Bioconductor Core Team

Examples

data(speciesMap)
sapply(speciesMap, class)   #       taxon     species
			    #    "integer" "character"
subset(speciesMap, species=="Homo sapiens")$taxon # [1] 9606