RBT: RBT: Replication Based Test
In AssotesteR: Statistical Tests for Genetic Association Studies

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1	RBT(y, X, perm = 100)

`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)

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

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

Gaston Sanchez

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

WSS, CMC

  ## 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)