getPermsBinaryExtantOnly: Calculates permuted correlation and enrichment statistics for...

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

Calculates permuted correlation and enrichment statistics for binary phenotype when performing an extant only analysis

Description

Calculates permuted correlation and enrichment statistics for binary phenotype when performing an extant only analysis

Usage

getPermsBinaryExtantOnly(
  numperms,
  fg_vec,
  sisters_list,
  root_sp,
  RERmat,
  trees,
  mastertree,
  permmode = "cc",
  method = "k",
  min.pos = 2,
  trees_list = NULL,
  calculateenrich = F,
  annotlist = NULL
)

Arguments

numperms	An integer number of permulations
fg_vec	A vector containing the tip foreground species
sisters_list	A list containing pairs of "sister species" in the foreground set (put NULL if empty)
root_sp	The species to root the tree on
RERmat	An RER matrix calculated using getAllResiduals.
trees	treesObj from readTrees
mastertree	A rooted, fully dichotomous tree derived from the treesObj master tree from readTrees. Must not contain species not in traitvec
permmode	Mode of binary permulation ("cc" for Complete Cases (default), "ssm" for Species Subset Match)
method	statistical method to use for correlations (set to "k" (default) for Kendall Tau test)
min.pos	minimum number of foreground species (default 2)
trees_list	A list containing the trees of all genes of interest (formatted like trees in treesObj from readTrees)
calculateenrich	A boolean variable indicating if null permulation p-values for enrichment statistics
annotlist	Pathway annotations

Value

A list object with enrichment statistics, correlation p-val, rho, and correlation effect size

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