RefFreeEWAS (version 2.2)

BootRefFreeEwasModel: Bootstrap for Reference-Free EWAS Model

Description

Bootstrap procedure for reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types.

Usage

BootRefFreeEwasModel(mod, nboot)

Arguments

mod

model object of class RefFreeEwasModel (generated with smallOutput=FALSE).

nboot

Number of bootstrap samples to generate

Value

An array object of class “BootRefFreeEwasModel”. Bootstraps are generated for both Beta and Bstar.

Details

Generates the bootstrap samples for the reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types.

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)

# }
# NOT RUN {
  tmpDesign <- cbind(1, rfEwasExampleCovariate)
  tmpBstar <- (rfEwasExampleBetaValues <!-- %*% tmpDesign %*% solve(t(tmpDesign)%*%tmpDesign)) -->

  EstDimRMT(rfEwasExampleBetaValues-tmpBstar <!-- %*% t(tmpDesign))$dim -->
# }
# NOT RUN {
test <- RefFreeEwasModel(
  rfEwasExampleBetaValues,
  cbind(1,rfEwasExampleCovariate),
  4)

testBoot <- BootRefFreeEwasModel(test,10)
summary(testBoot)

# }