createLineageLookup

Create a look up table that goes from TaxID, to Lineage

Usage

createLineageLookup(
  lineage_file = here("data/rankedlineage.dmp"),
  outfile,
  taxonomic_rank = "phylum"
)

Arguments

lineage_file

Path to the rankedlineage.dmp file containing taxid's and their corresponding taxonomic rank. rankedlineage.dmp can be downloaded at https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/

outfile

File the resulting lineage lookup table should be written to

taxonomic_rank

The upperbound of taxonomic rank that the lineage includes. The lineaege will include superkingdom>...>taxonomic_rank. Choices include: "supperkingdom", "phylum", "class","order", "family", "genus", and "species"

Value

A tibble containing the tax IDs and their respective lineages up to the specified taxonomic rank, saved as a tab-separated file.

Author

Samuel Chen

Examples

if (FALSE) { # \dontrun{
createLineageLookup(lineage_file = "data/rankedlineage.dmp", 
                     outfile = "data/lineage_lookup.tsv", 
                     taxonomic_rank = "family")
} # }