calculateCorPermuted: Calculate permulation correlation statistics

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

Calculate permulation correlation statistics

Description

Calculate permulation correlation statistics

Usage

calculateCorPermuted(
  permulated.paths,
  RERmat,
  min.sp = 10,
  min.pos = 2,
  method = "k"
)

Arguments

permulated.paths	A nested list of permulated paths (e.g., output of calculatePermulatedPaths_apply
RERmat	An RER matrix calculated using getAllResiduals.
min.sp	Minimum number of species that must be present for a gene
min.pos	Minimum number of species that must be present in the foreground (non-zero phenotype values)
method	Method used to compute correlations. Accepts the same arguments as cor. Set to "auto" to select automatically based on the number of unique values in charP. This will also auto set the winsorization for Pearson correlation. Set winsorizetrait=some number and winsorizeRER=some number to override

Value

A nested list containing the correlation statistics for the permulations

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