getPermsContinuousExtantOnly: 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 an extant only analysis

Description

Calculates permuted correlation and enrichment statistics for an extant only analysis

Usage

getPermsContinuousExtantOnly(
  numperms,
  traitvec,
  RERmat,
  annotlist,
  trees,
  mastertree,
  calculateenrich = T,
  type = "simperm",
  winR = 3,
  winT = 3,
  method = "p",
  min.pos = 0
)

Arguments

numperms	An integer number of permulations
traitvec	A named phenotype vector
RERmat	An RER matrix calculated using getAllResiduals
annotlist	Pathway annotations
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
calculateenrich	A boolean variable indicating if null permulation p-values for enrichment statistics
type	One of "simperm", "sim", or "perm" for permulations, simulations, or permutations, respectively
winR	Integer winzorization value for RERmat
winT	Integer winzorization value for trait
method	statistical method to use for correlations
min.pos	minimum foreground species - should be set to 0

Value

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

Note

winsorize is in terms of number of observations at each end, NOT quantiles

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