GenomeInfoDb-package {GenomeInfoDbData} | R Documentation |
Species and taxonomy ID look up tables
Description
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.
Usage
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(specData)
sapply(specData, class) # tax_id genus species
# "integer" "factor" "character"
subset(specData, c(genus=="Homo" & species=="sapiens"))$tax_id # [1] 9606
[Package GenomeInfoDbData version 1.2.8 Index]