AssotesteR (version 0.1-10)

BST: BST: Bayesian Score Test

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)

Value

"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

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.

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)