root_tree_in_outgroup: Root phylogenetic tree of a phyloseq object
In simeross/CuPhyR: Custom Functions for Microbiome Analysis with Phyloseq
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
View source: R/root_tree_in_outgroup.R
Description
This funtion defines the leaf with the longest path as the root of the phylogenetic tree.
This makes results reproducible by avoiding the behaviour of some functions that would otherwise pick a
random leaf as the root of an unrooted phylogenetic tree.
Based on answers in https://github.com/joey711/phyloseq/issues/597. The function requires the packages
'ape' and 'data.table' to be installed.
Usage
1
root_tree_in_outgroup(physeq = ps)
Arguments
physeq
a phyloseq object containing a phylogenetic tree to be rooted in an outgroup.
Value
a rooted phylogenetic tree.
Author(s)
Simeon Rossmann
See Also
Discussion and answers in [related GitHub thread](https://github.com/joey711/phyloseq/issues/597)
Examples
1
phyloseq::phy_tree(ps) <- root_tree_in_outgroup(physeq = ps)
simeross/CuPhyR documentation built on April 1, 2020, 10:28 a.m.
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Description Usage Arguments Value Author(s) See Also Examples
View source: R/root_tree_in_outgroup.R
Description
This funtion defines the leaf with the longest path as the root of the phylogenetic tree. This makes results reproducible by avoiding the behaviour of some functions that would otherwise pick a random leaf as the root of an unrooted phylogenetic tree. Based on answers in https://github.com/joey711/phyloseq/issues/597. The function requires the packages 'ape' and 'data.table' to be installed.
Usage
1 | root_tree_in_outgroup(physeq = ps)
|
Arguments
physeq |
a phyloseq object containing a phylogenetic tree to be rooted in an outgroup. |
Value
a rooted phylogenetic tree.
Author(s)
Simeon Rossmann
See Also
Discussion and answers in [related GitHub thread](https://github.com/joey711/phyloseq/issues/597)
Examples
1 | phyloseq::phy_tree(ps) <- root_tree_in_outgroup(physeq = ps)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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