WSS: WSS: Weighted Sum Statistic

In AssotesteR: Statistical Tests for Genetic Association Studies

Description

The WSS method has been proposed by Madsen and Browning (2009) as a pooling approach. In WSS, rare-variant counts within the same gene for each individual are accumulated rather than collapsing on them. Second, it introduces a weighting term to emphasize alleles with a low frequency in controls. Finally, the scores for all samples are ordered, and the WSS is computed as the sum of ranks for cases. The significance is determined by a permutation procedure.

Usage

  WSS(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:

wss.stat	wss statistic
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

Madsen BE, Browning SR (2009) A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic. PLoS Genetics, 5(2): e1000384

See Also

CMC

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 WSS with 500 permutations
  mywss = WSS(phenotype, genotype, perm=500)
  mywss
  
## End(Not run)

Example output

Loading required package: mvtnorm

 	 WSS: Weighted Sum Statistic 

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

  wss.stat    perm.pval   
247969.500        0.802   

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