R: WST: Weighted Score Test

WST {AssotesteR} | R Documentation

## WST: Weighted Score Test

### Description

The WST method has been proposed by Wang and Elston (2007) and it can be seen as a fixed effects method with transformed predictors based on Fourier Transformations. WST is based on Fourier Transform (FT) coefficients to globally test a set of correlated genetic variants (e.g. SNPs). The sequence of genetic variants values is transformed into a sequence of numbers by discrete FT, but only the real parts of the FT coefficients are taken into account. A weighted score statistic of the FT components is calculated, which follows a standard normal distribution under the null hypothesis

### Usage

      WST(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. NO missing data is allowed
`perm` | positive integer indicating the number of permutations (100 by default)

### Details

This function does not allow missing genotypes

### Value

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

`wst.stat` | wst statistic
`asym.pval` | asymptotic p-value
`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

Wang T, Elston C (2007) Improved Power by Use of a Weighted Score Test for Linkage Disequilibrium Mapping. The American Journal of Human Genetics, 80: 353-360

### See Also

`SCORE`, `SUM`

### 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 WST with 500 permutations
      mywst = WST(phenotype, genotype, perm=500)
      mywst

    ## End(Not run)

[Package AssotesteR version 0.1-10 Index]