taxonkit_filter: Filter TaxIDs based on Taxonomic Ranks

In pctax: Professional Comprehensive Omics Data Analysis

Filter TaxIDs based on Taxonomic Ranks

Description

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

Usage

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.

Examples

## Not run: 
taxids2 <- system.file("extdata/taxids2.txt", package = "pctax")
taxonkit_filter(taxids2, lower_than = "genus")

## End(Not run)

pctax documentation built on May 29, 2024, 10:03 a.m.