ORWSS: ORWSS: Odds Ratio Weighted Sum Statistic

In gastonstat/AssotesteR: Statistical Tests for Genetic Association Studies

Description

The ORWSS method has been proposed by Feng et al (2011) and it is based on a weighted sum statistic like the WSS method of Madsen and Browning (2009). ORWSS uses the logarithm of the odds ratio of a genetic variant as the weight for that variant, rather than the variance estimated in controls.

Usage

  ORWSS(y, X, c.param = NULL, 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
c.param	optional value to specify the c parameter. See reference Feng et al, 2011
perm	positive integer indicating the number of permutations (100 by default)

Details

When c.param=NULL, the weights of the sum statistic are simply the logarithm of the amended Odds Ratio of each variant (as in Dai et al 2012). Alternative values like c.param=1.64 or c.param=1.28 are suggested in Feng et al (2011).

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:

orwss.stat	orwss 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

Feng T, Elston RC, Zhu X (2011) Detecting Rare and Common Variants for Complex Traits: Sibpair and Odds Ratio Weighted Sum Statistics (SPWSS, ORWSS). Genetic Epidemiology, 35: 398-409

Dai Y, Jiang R, Dong J (2012) Weighted selective collapsing strategy for detecting rare and common variants in genetic association study. BMC Genetics, 13:7

See Also

WSS

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 ORWSS with c.param=NULL and 500 permutations
  myorwss1 = ORWSS(phenotype, genotype, c.param=NULL, perm=100)
  myorwss1

  # apply ORWSS with c.param=1.64 (see Feng et al 2011)
  myorwss2 = ORWSS(phenotype, genotype, c.param=1.64, perm=100)
  myorwss2
  
## End(Not run)

gastonstat/AssotesteR documentation built on May 16, 2019, 5:43 p.m.