taxonkit_list: Taxonkit list

In pctax: Professional Comprehensive Omics Data Analysis

Taxonkit list

Description

This function uses Taxonkit to perform the "list" operation, which retrieves information about taxa based on their TaxIDs.

Usage

taxonkit_list(
  ids,
  indent = "  ",
  json = FALSE,
  show_name = FALSE,
  show_rank = FALSE,
  data_dir = NULL
)

Arguments

ids	A character vector of TaxIDs to retrieve information for.
indent	The indentation string to use for pretty-printing the output. Default is " ".
json	Logical value indicating whether to output the result in JSON format. Default is FALSE.
show_name	Logical value indicating whether to show the scientific names of taxa. Default is FALSE.
show_rank	Logical value indicating whether to show the ranks of taxa. Default is FALSE.
data_dir	directory containing nodes.dmp and names.dmp (default "/Users/asa/.taxonkit")

Value

The output of the Taxonkit list operation.

See Also

Other Rtaxonkit: check_taxonkit(), download_taxonkit_dataset(), install_taxonkit(), name_or_id2df(), taxonkit_filter(), taxonkit_lca(), taxonkit_lineage(), taxonkit_name2taxid(), taxonkit_reformat()

Examples

## Not run: 
taxonkit_list(ids = c(9605), indent = "-", show_name = TRUE, show_rank = TRUE)

## End(Not run)

pctax documentation built on April 4, 2025, 2:26 a.m.