| Title: | Species and taxonomy ID look up tables used by GenomeInfoDb |
|---|---|
| Description: | Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package. |
| Authors: | Bioconductor Core Team |
| Maintainer: | Bioconductor Maintainer <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.2.13 |
| Built: | 2024-11-05 23:12:55 UTC |
| Source: | https://github.com/Bioconductor/GenomeInfoDbData |
This package contains one mapping object:
specData: A data frame with columns ‘tax_id’, ‘genus’, and ‘species’. Used to retrieve taxonomy ID by species and returns list of available species.
data(specData)data(specData)
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.
Bioconductor Core Team
data(specData) sapply(specData, class) # tax_id genus species # "integer" "factor" "character" subset(specData, c(genus=="Homo" & species=="sapiens"))$tax_id # [1] 9606data(specData) sapply(specData, class) # tax_id genus species # "integer" "factor" "character" subset(specData, c(genus=="Homo" & species=="sapiens"))$tax_id # [1] 9606