cum_prop: Taxon Proportion for All Non-rooted Nodes in a Phylogenetic...
In songbiostat/MiAF: Microbiome Adaptive Fisher Test
Description
Usage
Arguments
Value
Description
Calculate the taxon proportion for all non-rooted nodes
in a phylogenetic tree, as well as return the labels for those nodes.
The code is adapted from GUniFrac package contributed by
Jun Chen (Jun 12, 2015).
Usage
1
cum_prop(otu.tab, tree)
Arguments
otu.tab
OTU count table.
Row - n samples, column - OTUs
tree
A rooted phylogenetic tree of R class "phylo".
Value
A list containing the following elements:
cum
Taxon proportion for all non-rooted nodes.
The nodes are arranged in the same order as the second column of tree$edge.
br.len
Branch length for all non-rooted nodes.
cum.labels
Labels for all non-rooted nodes.
If node.label is not provided by the tree of R class "phylo", we assign "Node k" to the kth node.
songbiostat/MiAF documentation built on Feb. 18, 2022, 10:29 p.m.
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Description Usage Arguments Value
Description
Calculate the taxon proportion for all non-rooted nodes in a phylogenetic tree, as well as return the labels for those nodes. The code is adapted from GUniFrac package contributed by Jun Chen (Jun 12, 2015).
Usage
1 | cum_prop(otu.tab, tree)
|
Arguments
otu.tab |
OTU count table. Row - n samples, column - OTUs |
tree |
A rooted phylogenetic tree of R class "phylo". |
Value
A list containing the following elements:
cum |
Taxon proportion for all non-rooted nodes. The nodes are arranged in the same order as the second column of tree$edge. |
br.len |
Branch length for all non-rooted nodes. |
cum.labels |
Labels for all non-rooted nodes. If node.label is not provided by the tree of R class "phylo", we assign "Node k" to the kth node. |
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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