GenomeInfoDb-package {GenomeInfoDbData} | R Documentation |
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.
data(speciesMap) data(validTaxIds) 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(speciesMap) sapply(speciesMap, class) # taxon species # "integer" "character" subset(speciesMap, species=="Homo sapiens")$taxon # [1] 9606