AssotesteR (version 0.1-10)

WST: 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)

Value

"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

Details

This function does not allow missing genotypes

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)