generatePermulatedBinPhen: Produces binary permulations for a gene

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Produces binary permulations for a gene

Description

Produces binary permulations for a gene

Usage

generatePermulatedBinPhen(
  tree,
  numperms,
  trees,
  root_sp,
  fg_vec,
  sisters_list,
  pathvec,
  permmode = "cc"
)

Arguments

tree	Tree of the gene of interest (if permmode="cc", set this as the masterTree in trees (i.e., the output from readTrees))
numperms	An integer number of permulations
trees	treesObj from readTrees
root_sp	The species to root the tree on
fg_vec	A vector containing the foreground species
sisters_list	A list containing pairs of "sister species" in the foreground set (put NULL if empty)
pathvec	A path vector generated from the real set of foreground animals

Value

output.list a list containing the set of binary permulated trees

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.