getId2: Find a given taxa by name
In taxonomizr: Functions to Work with NCBI Accessions and Taxonomy

getId2

R Documentation

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. NOTE: This function is now deprecated for getId (using SQLite rather than data.table).

Usage

getId2(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)

Examples

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|"
)
tmpFile<-tempfile()
writeLines(namesText,tmpFile)
names<-read.names(tmpFile)
getId2('Bacteria',names)
getId2('Not a real name',names)
getId2('Multi',names)

taxonomizr documentation built on Feb. 16, 2023, 6:25 p.m.