getPermsBinaryFudged: 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 (does not enforce matching structure of sister species, but maintains internal & tips foreground counts within a fudge of the original tree)

Description

Calculates permuted correlation and enrichment statistics for binary phenotype (does not enforce matching structure of sister species, but maintains internal & tips foreground counts within a fudge of the original tree)

Usage

getPermsBinaryFudged(
  fgdspecs,
  RERs,
  trees,
  useSpecies,
  ntrees,
  root,
  fudge = 5,
  cors,
  phenvec
)

Arguments

fgdspecs	A vector containing the tip foreground species
RERs	An RER matrix calculated using getAllResiduals.
trees	treesObj from readTrees
useSpecies	A vector of species to include
ntrees	An integer number of permulations
root	The species to root the tree on
fudge	The number up to which the permulated tree can differ in total foreground species
cors	The gene correlation results from correlateWithBinaryPhenotype
phenvec	A named vector of the phenotype

Value

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

nclark-lab/RERconverge documentation built on June 9, 2025, 6:02 a.m.