R: RBT: Replication Based Test

RBT {AssotesteR} | R Documentation

## RBT: Replication Based Test

### Description

The Replication-Based Test has been proposed by Ionita-Laza et al (2011). RBT is based on a weighted-sum statistic that is similar to a pooled association test but purposefully designed to deal with possibly different association directions. The significance of the statistic has to be calculated by permutations.

### Usage

      RBT(y, X, perm = 100)

### 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
`perm` | positive integer indicating the number of permutations (100 by default)

### Details

There is no imputation for the missing data. Missing values are simply ignored in the computations.

### Value

An object of class `"assoctest"`, basically a list with the following elements:

`rbt.stat` | rbt statistic
`perm.pval` | permuted p-value
`args` | descriptive information with number of controls, cases, variants, and permutations
`name` | name of the statistic

### Author(s)

Gaston Sanchez

### References

Ionita-Laza I, Buxbaum JD, Laird NM, Lange C (2011) A New Testing Strategy to Identify Rare Variants with Either risk or Protective Effects on Disease. PLoS Genetics, 7(2): e1001289

### See Also

`WSS`, `CMC`

### Examples

      ## Not run:

      # number of cases
      cases = 500

      # number of controls
      controls = 500

      # 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(123)
      genotype = matrix(rbinom(total*10, 2, 0.05), nrow=total, ncol=10)

      # apply RBT with 500 permutations
      myrbt = RBT(phenotype, genotype, perm=500)
      myrbt

    ## End(Not run)

[Package AssotesteR version 0.1-10 Index]