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

In RefFreeEWAS: EWAS using Reference-Free DNA Methylation Mixture Deconvolution

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

Details

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

Value

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

Author(s)

E. Andres Houseman

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

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)))

RefFreeEWAS documentation built on May 2, 2019, 5:52 a.m.