taxonomizr (version 0.2.2)

getId: Find a given taxa by name

Description

Find a taxa by string in the NCBI taxonomy. Note that NCBI species are stored as Genus species e.g. "Bos taurus". Ambiguous taxa names will return a comma concatenated string e.g. "123,234" and generate a warning.

Usage

getId(taxa, taxaNames)

Arguments

taxa

a vector of taxonomic names

taxaNames

a names data.table from read.names

Value

a vector of character strings giving taxa IDs (potentially comma concatenated for any taxa with ambiguous names)

See Also

read.names

Examples

# NOT RUN {
namesText<-c(
  "1\t|\tall\t|\t\t|\tsynonym\t|",
  "1\t|\troot\t|\t\t|\tscientific name\t|",
  "3\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "4\t|\tMulti\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tBacteria\t|\tBacteria <prokaryotes>\t|\tscientific name\t|",
  "2\t|\tMonera\t|\tMonera <Bacteria>\t|\tin-part\t|",
  "2\t|\tProcaryotae\t|\tProcaryotae <Bacteria>\t|\tin-part\t|"
)
names<-read.names(textConnection(namesText))
getId('Bacteria',names)
getId('Not a real name',names)
getId('Multi',names)
# }