checkNewick: Check the validity of input newick tree

In PhyloProfile: PhyloProfile

Description

Check the validity of input newick tree

Usage

checkNewick(tree, inputTaxonID = NULL)

Arguments

tree	input newick tree
inputTaxonID	list of all input taxon IDs for the phylogenetic profiles

Value

Possible formatting error of input tree. 0 = suitable tree for using with PhyloProfile, 1 = missing parenthesis; 2 = missing comma; 3 = tree has singleton; or a list of taxa that do not exist in the input phylogenetic profile.

Author(s)

Vinh Tran [e-mail]

See Also

getInputTaxaID for getting input taxon IDs, ppTree for an example of input tree

Examples

data("ppTree", package="PhyloProfile")
checkNewick(ppTree, c("ncbi3702", "ncbi3711", "ncbi7029"))

Example output

[1] "ncbi2234; ncbi329726"

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.