WST: WST: Weighted Score Test
In gastonstat/AssotesteR: Statistical Tests for Genetic Association Studies

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

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

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

This function does not allow missing genotypes

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

Gaston Sanchez

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

SCORE, SUM

  ## 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)