generatePermulatedBinPhenSSMBatched: Produces binary SSM permulations for a list of genes

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

Produces binary SSM permulations for a list of genes

Description

Produces binary SSM permulations for a list of genes

Usage

generatePermulatedBinPhenSSMBatched(
  trees_list,
  numperms,
  trees,
  root_sp,
  fg_vec,
  sisters_list,
  pathvec
)

Arguments

trees_list	A list containing the trees of all genes of interest (formatted like trees in treesObj 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

simPhenoList A list containing binary permulated trees for each gene

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