getLineage: get NCBI taxonomy rank lineages

Description Usage Arguments Examples

View source: R/taxonomy.R

Description

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

Usage

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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

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

raim/ncbitax documentation built on Nov. 5, 2019, 2:08 a.m.