correlateWithContinuousPhenotype: Computes the association statistics between RER from...

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

Computes the association statistics between RER from getAllResiduals and a phenotype paths vector for a continuous phenotype made with char2Paths

Description

Computes the association statistics between RER from getAllResiduals and a phenotype paths vector for a continuous phenotype made with char2Paths

Usage

correlateWithContinuousPhenotype(
  RERmat,
  charP,
  min.sp = 10,
  winsorizeRER = 3,
  winsorizetrait = 3
)

Arguments

RERmat	RER matrix returned by getAllResiduals
charP	phenotype vector returned by tree2Paths or char2Paths
min.sp	Minimum number of species that must be present for a gene
winsorizeRER	Winsorize RER values before computing Pearson correlation. winsorizeRER=3 will set the 3 most extreme values at each end of each RER row to the the value closest to 0.
winsorizetrait	Winsorize trait values before computing Pearson correlation. winsorizetrait=3 will set the 3 most extreme values of the trait values to the value closest to 0.
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

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