root_phyloseq_tree: Root phyloseq tree.

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

A function for rooting and saving a phylogenetic tree.

Usage

root_phyloseq_tree(phyloseq_object, tree_path, save_rooted_tree,
  recursive = TRUE)

Arguments

phyloseq_object	A phyloseq object that contains a phylogenetic tree.
tree_path	The path to the existing or desired phylogenetic tree file.
save_rooted_tree	A logical that determines weather or not the rooted tree is saved.
recursive	If the directory doesn't exist, create the parent directories that don't exist as well, Default: TRUE

Details

This function is a helper function to get a proper phyloseq object for downstream analysis. Some analyses require a rooted tree. The function saves the rooted tree in the phyloseq object. It can also save the tree as a file if desired.

Value

Returns a phyloseq object with a rooted tree.

See Also

root, read.tree, write.tree

phy_tree

fileutils

Other Phylogenetic Tree Manipulators: pick_new_outgroup, root_by_longest_edge

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.