RefFreeEWAS (version 2.2)

omnibusBoot: Bootstrap-based omnibus test of significance across all features

Description

Support for bootstrap-based omnibus test of significance accounting for correlation.

Usage

omnibusBoot(est, boots, denDegFree)

Arguments

est

Vector of m estimates, one for each of m features.

boots

Matrix (m x R) of bootstrap samples corresponding to the estimates

denDegFree

Single number representing the denominator degrees-of-freedom for computing p-values

Value

A single number representing the p-value for the omnibus test over all features.

Details

Returns one omnibus p-value based on Kolmogorov-Smirnov distance from a uniform distribution

References

Houseman EA, Molitor J, and Marsit CJ (2014), Reference-Free Cell Mixture Adjustments in Analysis of DNA Methylation Data. Bioinformatics, doi: 10.1093/bioinformatics/btu029.

See Also

RefFreeEwasModel

Examples

# NOT RUN {
data(RefFreeEWAS)

test <- RefFreeEwasModel(
  rfEwasExampleBetaValues,
  cbind(1,rfEwasExampleCovariate),
  4)

testBoot <- BootRefFreeEwasModel(test,10)
summary(testBoot)
omnibusBoot(test$Beta[,2], testBoot[,2,"B",],-diff(dim(test$X))) 
omnibusBoot(test$Bstar[,2], testBoot[,2,"B*",],-diff(dim(test$X)))
# }