TTEST {AssotesteR} | R Documentation |
Generalized T2 test for testing association between genotype variants and binary trait (case-control)
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
## 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)