R: WSS: Weighted Sum Statistic

WSS {AssotesteR} | R Documentation

## WSS: Weighted Sum Statistic

### 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)

[Package AssotesteR version 0.1-10 Index]