simTest: Simulation Testing.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Simulation Testing.

Description

Generic simulation-testing function used to validate treeWAS performance on simulated datasets. Not designed for public use!

Usage

simTest(
  set.number = 3,
  n.reps = 1,
  set.seed.as = "file.number",
  working.dir = "~/",
  from.file = FALSE,
  file.n = NULL,
  Windows = FALSE,
  cluster = FALSE,
  n.ind = 100,
  n.snps = 10000,
  n.subs = treeWAS::dist_0.01,
  n.phen.subs = 15,
  n.snps.assoc = 10,
  assoc.prob = 90,
  grp.min = 0.25,
  s = 20,
  af = 10,
  coaltree = TRUE,
  p.value = 0.01,
  p.value.correct = "bonf",
  p.value.by = "count",
  sim.n.snps = 1e+05,
  treeWAS.test = c("terminal", "simultaneous", "subsequent"),
  snps.reconstruction = "parsimony",
  phen.reconstruction = "parsimony"
)

Arguments

test	A character string or vector containing one or more of the following available tests of association: "terminal", "simultaneous", "subsequent", "cor", "fisher". By default, the first three tests are run. See details for more information on what these tests do and when they may be appropriate.

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.