MULTI {AssotesteR} | R Documentation |
Performs multiple association tests.
MULTI(y, X, tests, maf = 0.05, perm = 100, weights = NULL, c.param = NULL)
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 |
tests |
character vector with names of the tests to be applied |
maf |
numeric value indicating the minor allele frequency threshold for rare variants ( |
perm |
positive integer indicating the number of permutations (100 by default) |
weights |
optional vector of weights for the variants ( |
c.param |
Optional value to specify the |
The available tests are: "WSS", "ORWSS", "RWAS", "CMC", "CMAT", "CALPHA", "RBT", "SCORE", "SUM", "SSU", "SSUW", "UMINP", "BST", "WST", "RVT1", "RVT2", "VT"
There is no imputation for the missing data. Missing values are simply ignored in the computations.
A data frame with test statistics and permutated p-values
Gaston Sanchez
## Not run: # number of cases cases = 250 # number of controls controls = 250 # 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(1234) genotype = matrix(rbinom(total*10, 2, 0.051), nrow=total, ncol=10) # apply MULTI with "BST", "CMC", "RWAS" and 100 permutations mymulti1 = MULTI(phenotype, genotype, c("BST", "CMC", "RWAS"), perm=100) # this is what we get mymulti1 # create list with the following tests test_list = c("BST", "CMC", "CMAT", "CALPHA", "ORWSS", "RWAS", "RBT", "SCORE", "SUM", "SSU", "SSUW", "UMINP", "WSS", "WST") # apply MULTI with 100 permutations mymulti2 = MULTI(phenotype, genotype, test_list, perm=100) # this is what we get mymulti2 ## End(Not run)