checkNewick: Check the validity of input newick tree

Description Usage Arguments Value Author(s) See Also Examples

View source: R/parsePhylotree.R

Description

Check the validity of input newick tree

Usage

1
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 tran@bio.uni-frankfurt.de

See Also

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

Examples

1
2
data("ppTree", package="PhyloProfile")
checkNewick(ppTree, c("ncbi3702", "ncbi3711", "ncbi7029"))

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