assoc.test: Run a test of association between SNPs and a phenotype.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Run a test of association between SNPs and a phenotype.

Description

Run one of five tests of association between each column of a SNPs matrix and a phenotype (some tests only implemented for binary SNPs and phenotype).

Usage

assoc.test(
  snps,
  phen,
  tree = NULL,
  test = c("terminal", "simultaneous", "subsequent"),
  correct.prop = FALSE,
  categorical = FALSE
)

Arguments

snps	A matrix containing the real snps.
phen	A factor or vector containing the phenotype (only allowed to contain two levels for now).
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.