MULTI: MULTI: Multiple Tests

In AssotesteR: Statistical Tests for Genetic Association Studies

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

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

  ## 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)

Example output

Loading required package: mvtnorm
       statistic pvalue
BST  -29.4522500   0.88
CMC    5.1401172   0.88
RWAS  -0.3977298   0.69
           statistic pvalue
BST      -29.4522500   0.85
CMC        5.1401172   0.83
CMAT       0.1105821   0.68
CALPHA   -78.0000000   0.92
ORWSS  59653.0000000   0.97
RWAS      -0.3977298   0.66
RBT        6.5835039   0.91
SCORE      5.8045202   0.84
SUM       -1.0670226   0.84
SSU       69.7500000   0.85
SSUW       5.5637025   0.84
UMINP      0.7928300   0.47
WSS    60918.0000000   0.94
WST       -0.9139190   0.86

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