Filter TaxIDs based on Taxonomic Ranks

This function uses the "taxonkit filter" command to filter TaxIDs based on taxonomic ranks.

taxonkit_filter(
  file_path,
  black_list = NULL,
  discard_noranks = FALSE,
  discard_root = FALSE,
  equal_to = NULL,
  higher_than = NULL,
  lower_than = NULL,
  rank_file = NULL,
  root_taxid = NULL,
  save_predictable_norank = FALSE,
  taxid_field = NULL,
  text = FALSE,
  data_dir = NULL
)

Arguments

file_path

The path to the input file containing TaxIDs. Or file text (text=TRUE)

black_list

A character vector specifying the ranks to discard.

discard_noranks

Logical value indicating whether to discard all ranks without order (default is FALSE).

discard_root

Logical value indicating whether to discard the root taxid (default is FALSE).

equal_to

A character vector specifying the ranks for which TaxIDs should be equal to.

higher_than

The rank above which the TaxIDs should be (exclusive).

lower_than

The rank below which the TaxIDs should be (exclusive).

rank_file

The path to a user-defined ordered taxonomic ranks file.

root_taxid

The root taxid (default is 1).

save_predictable_norank

Logical value indicating whether to save some special ranks without order when using lower_than (default is FALSE).

taxid_field

The field index of the taxid in the input file (default is 1).

text

logical

data_dir

directory containing nodes.dmp and names.dmp (default "/Users/asa/.taxonkit")

Value

A character vector containing the output of the "taxonkit filter" command.

See also

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

Examples

if (FALSE) { # \dontrun{
taxids2 <- system.file("extdata/taxids2.txt", package = "pctax")
taxonkit_filter(taxids2, lower_than = "genus")
} # }