R: TTEST: Hotelling T2 Test

TTEST {AssotesteR} | R Documentation

## TTEST: Hotelling T2 Test

### Description

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

### Usage

      TTEST(y, X)

### Arguments

`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

### Details

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

### Value

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

### Author(s)

Gaston Sanchez

### References

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

### See Also

`CAST`

### Examples

      ## 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)

[Package AssotesteR version 0.1-10 Index]