AssotesteR (version 0.1-10)

TTEST: 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

Value

"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

Details

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

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)