MULTI: MULTI: Multiple Tests

Description Usage Arguments Details Value Author(s) Examples

View source: R/MULTI.R

Description

Performs multiple association tests.

Usage

1
  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

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.

Value

A data frame with test statistics and permutated p-values

Author(s)

Gaston Sanchez

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
  ## 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)

AssotesteR documentation built on May 2, 2019, 3:55 a.m.