taxonkit_lineage: Retrieve Taxonomic Lineage using taxonkit

In pctax: Professional Comprehensive Omics Data Analysis

Retrieve Taxonomic Lineage using taxonkit

Description

Retrieve Taxonomic Lineage using taxonkit

Usage

taxonkit_lineage(
  file_path,
  delimiter = ";",
  no_lineage = FALSE,
  show_lineage_ranks = FALSE,
  show_lineage_taxids = FALSE,
  show_name = FALSE,
  show_rank = FALSE,
  show_status_code = FALSE,
  taxid_field = 1,
  text = FALSE,
  data_dir = NULL
)

Arguments

file_path	The path to the input file with taxonomic IDs. Or file text (text=TRUE)
delimiter	The field delimiter in the lineage (default ";").
no_lineage	Logical, indicating whether to exclude lineage information (default: FALSE).
show_lineage_ranks	Logical, indicating whether to append ranks of all levels in the lineage (default: FALSE).
show_lineage_taxids	Logical, indicating whether to append lineage consisting of taxids (default: FALSE).
show_name	Logical, indicating whether to append scientific name (default: FALSE).
show_rank	Logical, indicating whether to append rank of taxids (default: FALSE).
show_status_code	Logical, indicating whether to show status code before lineage (default: FALSE).
taxid_field	The field index of taxid. 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 taxonomic lineage information.

Examples

## Not run: 
taxonkit_lineage("9606\n63221", show_name = TRUE, show_rank = TRUE, text = TRUE)

## End(Not run)

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