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Retrieve Taxonomic Ranks Using NCBI Taxonomy Tax IDs

Source: R/get_tax_by_taxID.R
get_tax_by_taxID.Rd

Retrieves complete taxonomy information for given NCBI Taxonomy Tax IDs by querying the NCBI database using the efetch command.

Usage

get_tax_by_taxID(
  organisms_taxIDs,
  parse_result = TRUE,
  verbose = "silent",
  env_name = "blastr-entrez-env"
)

Arguments

organisms_taxIDs

A character vector of NCBI Taxonomy Tax IDs for which to retrieve taxonomy information.

parse_result

Logical indicating whether to parse the taxonomy information into a tibble (TRUE, default) or return the raw output as returned by efetch (FALSE).

verbose

Character indicating whether to print verbose messages during the process. Default is "silent".

env_name

Character string specifying the name of the conda environment where efetch is installed. Default is "blastr-entrez-env".

Value

A tibble containing the taxonomic ranks for the given Tax IDs.

Examples

if (FALSE) { # \dontrun{
# Retrieve taxonomy for a single Tax ID
tax_info <- get_tax_by_taxID("9606") # Human

# Retrieve taxonomy for multiple Tax IDs
tax_ids <- c("9606", "10090", "10116") # Human, Mouse, Rat
tax_info <- get_tax_by_taxID(tax_ids)

# Get unparsed taxonomy result
raw_tax_info <- get_tax_by_taxID("9606", parse_result = FALSE)

# Enable verbose output
tax_info <- get_tax_by_taxID("9606", verbose = "output")
} # }