check_tree_clustering: Check for clustering on tree

In Snitkin-Lab-Umich/snitkitr: Functions Commonly Used in the Snitkin Lab

Description

This function is used to test for clustering of a certain epi factor on a phylogenetic tree.

Usage

check_tree_clustering(
  tree,
  isolate_labels,
  nperm = 1000,
  control_labels = NULL,
  plot_path = "cluster.pdf"
)

Arguments

tree	Tree to look for clustering on.
isolate_labels	Named vector of labels by which pure clusters are defined. Names must be equivalent to tree tip label names.
nperm	Number of permutations to perform.
control_labels	Named vector of labels known to cluster. Names must be equivalent to tree tip label names. This controls for clustering by requiring that the pure clusters must contain multiple of the control labels.
plot_path	Path to output histogram. No plot created if NA.

Value

Vector of real (1st element) and permuted (all other elements) pure cluster sizes.

Examples

tree = ape::rtree(50)
labs = sample(c(0,1),50,replace=TRUE)
names(labs) = tree$tip.label
check_tree_clustering(tree,labs,nperm=10)

Snitkin-Lab-Umich/snitkitr documentation built on April 21, 2021, 10:48 a.m.