SSU: SSU: Sum of Squared Score U Statistic
In AssotesteR: Statistical Tests for Genetic Association Studies

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

SSU has been proposed by Pan (2009) as a modified test based on the score-type U statistic (i.e. logistic regression). More specifically, SSU is a test based on the 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. In addition, SSU can also be regarded as a modification to the sum test.

1	SSU(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. Missing data is allowed
`perm`	positive integer indicating the number of permutations (100 by default)

There is no imputation for the missing data. Missing values are simply ignored in the computations.

An object of class "assoctest", basically a list with the following elements:

`ssu.stat`	ssu 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

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

SCORE, SUM, SSUW

  ## 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 SSU with 500 permutations
  myssu = SSU(phenotype, genotype, perm=500)
  myssu
  
## End(Not run)