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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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)
|
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