SSUW: SSUW: Weighted Sum of Squared Score U Statistic

In AssotesteR: Statistical Tests for Genetic Association Studies

Description

SSUW s been proposed by Pan (2009) as a modified test based on the score-type U statistic (i.e. logistic regression). More specifically, SSUW is a test based on a weighted sum of the squares of the marginal score statistics. Its null distribution have a quadratic form and can be approximated by a chi-square distribution.

Usage

  SSUW(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

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:

ssuw.stat	ssuw 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

Pan W (2009) Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genetic Epidemiology, 33: 497-507

Pan W, Han F, Shen X (2010) Test Selection with Application to Detecting Disease Association with Multiple SNPs. Human Heredity, 69: 120-130

See Also

SCORE, SSU, 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 SSUW with 500 permutations
  myssuw = SSUW(phenotype, genotype, perm=500)
  myssuw
  
## End(Not run)

Example output

Loading required package: mvtnorm

 	 SSUW: Weighted Sum of Squared Score 

Info: 
   cases  controls  variants   n.perms  
     500       500        10       500  

ssuw.stat   asym.pval   perm.pval   
 6.153771    0.800934    0.794000   

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