load all lower taxonomy ID (all descendants)

loadTaxIDAllLower loads all load all lower taxonomy ID for a given taxonomy ID

loadTaxIDAllLower(taxid, dir, with_description = F)

Arguments

file	directory where to save/look for the local copy

Value

loadTaxIDAllLower returns list containing the character vector of all lower taxonomy ID for a given taxonomy ID (saves it to a file) and the input taxonomy ID (taxid) and optionally, a data.table containing the description of all lower

Examples

# Find all human sub-species
loadTaxIDAllLower(taxid = 9606, dir = "./")
#> $AllLower
#> [1]  63221 741158
#> 
#> $input_taxid
#> [1] 9606
#> 
loadTaxIDAllLower(taxid = 9606, dir = "./", with_description = T)
#> $AllLower
#> [1]  63221 741158
#> 
#> $input_taxid
#> [1] 9606
#> 
#> $description
#>     Taxon Mnemonic                Scientific name      Common name Synonym
#> 1:  63221    HOMNE  Homo sapiens neanderthalensis      Neanderthal      NA
#> 2: 741158          Homo sapiens subsp. 'Denisova' Denisova hominin      NA
#>                                                                                        Other Names
#> 1:  Feldhofer 1; Homo neanderthalensis; Neandertal; Neandertal man; Neanderthal 1; Neanderthal man
#> 2: Denisovan; Denisovans; Homo sapiens ssp. 'Denisova'; Homo sapiens ssp. Denisova; Homo sp. Altai
#>     Reviewed       Rank
#> 1:  reviewed Subspecies
#> 2: annotated Subspecies
#>                                                                                                                                                       Lineage
#> 1: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
#> 2: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
#>    Parent Virus hosts
#> 1:   9606          NA
#> 2:   9606          NA
#>