getLineage: get NCBI taxonomy rank lineages

In raim/ncbitax: Simple base R parser for NCBI Taxonomy

Description

Returns a table with taxonomic lineages at the requested rank levels. A wrapper around getAllParents.

Usage

getLineage(ids, tax, ranks = c("phylum", "species"), names = FALSE,
  reduce = FALSE)

Arguments

ids	vector of taxon IDs
tax	NCBI taxonomy object
ranks	vector of ranks to retrieve
names	return taxon names instead of ids
reduce	call reduceTaxonomy before search; untested but this makes subsequent search faster by using getAllParents first to reduce taxonomy to sub-tree for ids

Examples

getLineage(c("1148","1140"), tax, names=TRUE,
         ranks=c("superkingdom","phylum","species"))

raim/ncbitax documentation built on Aug. 6, 2020, 7:29 a.m.