SUM: SUM: Sum Test
In AssotesteR: Statistical Tests for Genetic Association Studies

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

The SUM test has been proposed by Pan (2009) based on a modification of the Score. The idea behind the Sum Test is to test on only one parameter under the assumption of a common association strength between each of multiple genetic variants (e.g. SNPs) and the trait under analysis. The Sum test focuses on a scalar function of the multiple parameters with a resulting degree of freedom DF=1

1	SUM(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:

`sum.stat`	sum 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 Association with Multiple SNPs. Human Heredity, 69: 120-130

SCORE, SSU, SSUW, WST

  ## 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 SUM with 500 permutations
  mysum = SUM(phenotype, genotype, perm=500)
  mysum
  
## End(Not run)