GenomeInfoDb (version 1.8.3)

speciesMap: Species Mapper object and/or list of valid taxonomy Ids

Description

A data frame containing a mapping between NCBI Taxonomy IDs and species OR a list of valid taxomony IDs (pre-subsetted and cleaned up from that same data.frame).

The reason why is because sometimes we need the entire frame, but other times we only need the list of integers, (which is much smaller and loads much more quickly)

The specData object is an even more complex data.frame that returns genus and species separately.

Usage

data(speciesMap) data(validTaxIds)

Format

A data frame with 1416382 observations on the following 2 variables.

taxon

a numeric vector

species

a character vector

Examples

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