R: SEQSUM: Sequential Sum Score Test

SEQSUM {AssotesteR} | R Documentation

## SEQSUM: Sequential Sum Score Test

### Description

SEQSUM has been proposed by Basu and Pan (2011) as a modification of the Sum test based on a model selection approach, following a similar philosophy as the CARV and RARECOVER methods. Assuming that there are M variants, the main idea behind the Sequential Sum test is to associate a sign to each variant indicating whether it has a positive effect or a negative effect. In other words, the purpose is to give signs to the variants so they reflect their effect (positive or negative).

### Usage

      SEQSUM(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:

`seqsum.stat` | seqsum statistic
`perm.pval` | permuted p-value
`signs` | a numeric vector with signs for the variants (1=positive, -1=negative)
`args` | descriptive information with number of controls, cases, variants, and permutations
`name` | name of the statistic

### Author(s)

Gaston Sanchez

### References

Basu S, Pan W (2011) Comparison of Statistical Tests for Disease Association with Rare Variants. Genetic Epidemiology, 35: 606-619

### See Also

`SCORE`, `SUM`

### 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 SEQSUM with 500 permutations
      myseq = SEQSUM(phenotype, genotype, perm=500)
      myseq

    ## End(Not run)

[Package AssotesteR version 0.1-10 Index]