BST: BST: Bayesian Score Test

In AssotesteR: Statistical Tests for Genetic Association Studies

Description

BST is based on the test statistic of Goeman et al (2005) following a general empirical Bayes method to test on a large number of parameters in a logistic regression model. BST is closely related to the usual Score test, although it assumes an empirical Bayesian model with an independent prior on the genetic variant effects. The null distribution of the BST statistic is unknown and has to be estimated by permutation.

Usage

  BST(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

The BST statistic does not offer an asymptotic p-value. Permutations are required

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:

bst.stat	bst 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

Goeman JJ, van de Geer SA, van Houwelingen HC (2006) Testing against a high dimensional alternative. Journal of the Royal Statistical Society, 68: 477-493

Chapman J, Whittaker J (2008) Analysis of Multiple SNPs in a Candidate Gene or Region. Genetic Epidemiology, 32: 560-566

Pan W (2009) Asymptotic Tests of Association with Multiple SNPs in Linkage Disequilibrium. Genetic Epidemiology, 33: 497-507

See Also

SCORE

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 BST with 500 permutations
  mybst = BST(phenotype, genotype, perm=500)  
  mybst
  
## End(Not run)

AssotesteR documentation built on May 2, 2019, 3:55 a.m.