getParents: lineage retrieval

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

Description

Returns an edge table of the parent lineage until root.

Usage

getParents(id, tax, skip = NULL, root = "1", names = FALSE,
  verb = TRUE, dbug = FALSE)

Arguments

id	a single taxon ID
tax	NCBI taxonomy object
skip	edges table to skip, if the node id is already present, the recursive function is not called (used internally from getAllParents)
root	taxon ID of the taxonomic class to be considered as root
names	return taxon names instead of ids
verb	print progress messages
dbug	print debug messages

Examples

getParents("1140", tax)
getParents("1148", tax, root="1783272")
getParents("1048", tax, root="1783272") # root not in lineage!

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