correlateWithCategoricalPhenotype: 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 categorical phenotype made with char2PathsCategorical

Description

Computes the association statistics between RER from getAllResiduals and a phenotype paths vector for a categorical phenotype made with char2PathsCategorical

Usage

correlateWithCategoricalPhenotype(
  RERmat,
  charP,
  min.sp = 10,
  min.pos = 2,
  method = "kw"
)

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
min.pos	Minimum number of species that must be present in a category
method	Method used to compute correlations. Use "kw" to use Kruskil Wallis. Use "aov" to use ANOVA. It must be one of the strings "kw" or "aov".

Value

A list containing a list object with correlation values, p-values, and the number of data points used for each tree and a list of list objects for each pairwise test with correlation values and p-values.

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