tax2newick: convert NCBI taxonomy sub trees to newick format

Description Usage Arguments Examples

View source: R/taxonomy.R

Description

convert NCBI taxonomy sub trees to newick format

Usage

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tax2newick(ids, tax, names = FALSE, full = FALSE, ranks = FALSE,
  verb = FALSE, dbug = FALSE)

Arguments

ids

vector of taxon IDs

tax

NCBI taxonomy object

names

replace taxon IDs with names

full

if TRUE singleton nodes with only one child will NOT be collapsed

ranks

add rank information for nodes

verb

print progress messages

dbug

print debug messages

Examples

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new <- tax2newick(ids=c("1148","1140"), tax=tax, names=TRUE)

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