Calculate false discovery rate (FDR) on a tree structure

Calculate the false discovery rate on a tree structure, at either leaf or node level.

Usage

fdr(tree, truth, found, only.leaf = TRUE)

Arguments

tree

A phylo object.

truth

True signal nodes (e.g., nodes that are truly differentially abundant between experimental conditions). Note: when the FDR is requested at the leaf level (only.leaf = TRUE), the descendant leaves of the given nodes will be found and the FDR will be estimated on the leaf level.

found

Detected signal nodes (e.g., nodes that have been found to be differentially abundant via a statistical testing procedure). Note: when the FDR is requested at the leaf level (only.leaf = TRUE), the descendant leaves of the given nodes will be found out and the FDR will be estimated on the leaf level.

only.leaf

A logical scalar. If TRUE, the false discovery rate is calculated at the leaf (tip) level; otherwise it is calculated at the node level.

Value

The estimated false discovery rate.

Author

Ruizhu Huang

Examples

suppressPackageStartupMessages({
    library(ggtree)
    library(TreeSummarizedExperiment)
})

data(tinyTree)

## Two branches are truly differential
ggtree(tinyTree, branch.length = "none") +
   geom_text2(aes(label = node)) +
   geom_hilight(node = 16, fill = "orange", alpha = 0.3) +
   geom_hilight(node = 13, fill = "blue", alpha = 0.3)


## FDR at the leaf level if nodes 14 and 15 are called differential (1/8)
fdr(tree = tinyTree, truth = c(16, 13),
    found = c(15, 14), only.leaf = TRUE)
#>   fdr 
#> 0.125 

## FDR at the node level if nodes 14 and 15 are called differential (2/14)
fdr(tree = tinyTree, truth = c(16, 13),
    found = c(15, 14), only.leaf = FALSE)
#>       fdr 
#> 0.1428571