R: SSU: Sum of Squared Score U Statistic

SSU {AssotesteR} | R Documentation

## SSU: Sum of Squared Score U Statistic

### Description

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.

### Usage

      SSU(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:

`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

### 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`, `SUM`, `SSUW`

### 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 SSU with 500 permutations
      myssu = SSU(phenotype, genotype, perm=500)
      myssu

    ## End(Not run)

[Package AssotesteR version 0.1-10 Index]