ORWSS {AssotesteR} | R Documentation |
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.
ORWSS(y, X, c.param = NULL, 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 |
c.param |
optional value to specify the |
perm |
positive integer indicating the number of permutations (100 by default) |
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.
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 |
Gaston Sanchez
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
## 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)