Description Usage Arguments Details Value Author(s) References See Also Examples
UMINP is the Univariate minP that tests on each single genetic variant (e.g. SNP) one-by-one and then takes the minimum of their p-values, Its null distribution is based on numerical integration with respect to a multivariate normal distribution.
1 | UMINP(y, X, perm = 100)
|
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 |
perm |
positive integer indicating the number of permutations (100 by default) |
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:
uminp.stat |
uminp statistic |
asym.pval |
asymptotic p-value |
perm.pval |
permuted p-value |
args |
descriptive information with number of controls, cases, variants, and permutations |
name |
name of the statistic |
Gaston Sanchez
Pan W (2009) Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genetic Epidemiology, 33: 497-507
Pan W, Han F, Shen X (2010) Test Selection with Application to Detecting Disease Association with Multiple SNPs. Human Heredity, 69: 120-130
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 UMINP with 500 permutations
myuminp = UMINP(phenotype, genotype, perm=500)
myuminp
## End(Not run)
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