taxdumpSubset: Utilities for NCBI Taxdump

Description Usage Arguments See Also

View source: R/taxdumpSubset.R

Description

Get subset of a taxonomy table in parent-child format.

Usage

1
taxdumpSubset(tax, mrca, species, root = "tol", syn = FALSE)

Arguments

tax

Either an object of class megapteraProj or a data frame containing a taxonomy table in parent-child format as returned by dbReadTaxonomy.

mrca

A character string giving the most recent common ancestor (MRCA) of the subset.

species

A vector of mode "character" giving a subset of species names.

root

A character string choosing between "mrca" and "tol" (tree of life).

syn

Logical, indicating if synonyms should be returned in addition to accepted names; only has an effect if tax is of class megapteraProj.

See Also

dbReadTaxonomy, taxdumpChildren,taxdumpLineage, taxdumpAddNode, taxdump2phylo.


heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.