Description Usage Arguments Details Value Author(s) References See Also Examples
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.
1 |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ## 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)
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