taxdumpChangeParent: Utilities for NCBI Taxdump

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Change a node's parent in the NCBI taxonomy.

Usage

taxdumpChangeParent(x, taxon, new.parent, orphaned.parent = "synonym")

Arguments

x	An object of class megapteraProj or a data.frame a parent-child-format.
taxon	A character string giving the name of the taxon.
new.parent	A character string giving the name of the new parent taxon.
orphaned.parent	A character string indicating how to treat previous parent taxa, that do not have other children than "taxon", i.e. which are orphaned.

Details

Two choices are possible for orphaned.parent: (1) "synonym" will classify the previous, orphaned parent as a synonym of "new.parent", whereas (2) "delete" will simply delete the orphaned parent from the taxonomy.

Value

A data.frame in parent-child-format, if class(x) == "data.frame", or TRUE, if class(x) == "megapteraProj". In the latter case taxdumpChangeParent is called for its side effect on the taxonomy table of the database.

See Also

ncbiTaxonomy for downloading the NCBI taxonomy and dbReadTaxonomy for reading the project taxonomy; other taxdump-related tools: taxdumpChildren, taxdumpDropTip, taxdumpHigherRank, taxdumpMRCA, taxdumpSubset, taxdump2phylo and taxdump_isTerminal.

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