Compute Lowest Common Ancestor (LCA) of TaxIDs

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

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

if (FALSE) { # \dontrun{
taxonkit_lca("239934, 239935, 349741", text = TRUE, separator = ", ")
} # }