TTEST: TTEST: Hotelling T2 Test
In AssotesteR: Statistical Tests for Genetic Association Studies

Description Usage Arguments Details Value Author(s) References See Also Examples

Generalized T2 test for testing association between genotype variants and binary trait (case-control)

1	TTEST(y, X)

`y`	numeric vector with phenotype status: 0=controls, 1=cases. No missing data allowed
`X`	numeric matrix or data frame with genotype data coded as 0, 1, 2. Missing data is allowed

There is no imputation for the missing data. Missing values are simply ignored in the computations.

An object of class "assoctest", basically a list with the following elements:

`T2.stat`	T2 statistic
`asym.pval`	asymptotic p-value
`args`	descriptive information with number of controls, cases, variants, maf, and applied test
`name`	name of the statistic

Gaston Sanchez

Xiong M, Zhao J, Boerwinkle E (2002) Generalized T2 Test for Genome Association Studies. The American Journal of Human Genetics, 70: 1257 - 1268

CAST

  ## Not run: 
  
  # number of cases
  cases =500

  # number of controls
  controls = 500

  # total (cases + controls)
  total = cases + controls

  # phenotype vector
  phenotype = c(rep(1, cases), rep(0, controls))

  # genotype matrix with 10 variants (random data)
  set.seed(123)
  genotype = matrix(rbinom(total*10, 2, 0.05), nrow=total, ncol=10)

  # apply TTEST 
  myttest = TTEST(phenotype, genotype)
  myttest  
  
## End(Not run)