phyloseq: read_tree – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

read_tree

Somewhat flexible tree-import function

Description

This function is a convenience wrapper around the read.tree (Newick-format) and read.nexus (Nexus-format) importers provided by the ape-package. This function attempts to return a valid tree if possible using either format importer. If it fails, it silently returns NULL by default, rather than throwing a show-stopping error.

Usage

read_tree(treefile, errorIfNULL=FALSE, ...)

Arguments

`treefile`	(Required). A character string implying a file `connection` (like a path or URL), or an actual `connection`. Must be a Newick- or Nexus-formatted tree.
`errorIfNULL`	(Optional). Logical. Should an error be thrown if no tree can be extracted from the connection? Default is `FALSE`, indicating that `NULL` will be SILENTLY returned, rather than an error. Be cautious about this behavior. Useful for phyloseq internals, but might be hard to track in your own code if you're not aware of this “no error by default” setting. If this is a problem, change this value to `TRUE`, and you can still use the function.
`...`	(Optional). Additional parameter(s) passed to the relevant tree-importing function.

Value

If successful, returns a phylo-class object as defined in the ape-package. Returns NULL if neither tree-reading function worked.

Examples

read_tree(system.file("extdata", "esophagus.tree.gz", package="phyloseq"))
read_tree(system.file("extdata", "GP_tree_rand_short.newick.gz", package="phyloseq"))

phyloseq

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23