taxonkit_lca: Compute Lowest Common Ancestor (LCA) of TaxIDs

In pctax: Professional Comprehensive Omics Data Analysis

Compute Lowest Common Ancestor (LCA) of TaxIDs

Description

This function uses the "taxonkit lca" command to compute the Lowest Common Ancestor (LCA) of TaxIDs.

Usage

taxonkit_lca(
  file_path,
  buffer_size = "1M",
  separator = " ",
  skip_deleted = FALSE,
  skip_unfound = FALSE,
  taxids_field = NULL,
  text = FALSE,
  data_dir = NULL
)

Arguments

file_path	The path to the input file containing TaxIDs. Or file text (text=TRUE)
buffer_size	The size of the line buffer (supported units: K, M, G).
separator	The separator for TaxIDs.
skip_deleted	Whether to skip deleted TaxIDs and compute with the remaining ones.
skip_unfound	Whether to skip unfound TaxIDs and compute with the remaining ones.
taxids_field	The field index of TaxIDs. Input data should be tab-separated (default 1).
text	logical
data_dir	directory containing nodes.dmp and names.dmp (default "/Users/asa/.taxonkit")

Value

A character vector containing the computed LCAs.

See Also

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

Examples

## Not run: 
taxonkit_lca("239934, 239935, 349741", text = TRUE, separator = ", ")

## End(Not run)

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