R: MULTI: Multiple Tests

MULTI {AssotesteR} | R Documentation

## 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`

### 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)

[Package AssotesteR version 0.1-10 Index]