AssotesteR (version 0.1-10)

MULTI: MULTI: Multiple Tests

Description

Performs multiple association tests.

Usage

MULTI(y, X, tests, maf = 0.05, perm = 100, weights = NULL, c.param = NULL)

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

tests

character vector with names of the tests to be applied

maf

numeric value indicating the minor allele frequency threshold for rare variants (maf=0.05 by default)

perm

positive integer indicating the number of permutations (100 by default)

weights

optional vector of weights for the variants (NULL by default

c.param

Optional value to specify the c parameter when applying ORWSS

Value

Details

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.

Examples

  ## 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)