RefFreeEWAS: BootRefFreeEwasModel – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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

Details

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

Value

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

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.

Examples

data(RefFreeEWAS)

## Not run: 
  tmpDesign <- cbind(1, rfEwasExampleCovariate)
  tmpBstar <- (rfEwasExampleBetaValues 

  EstDimRMT(rfEwasExampleBetaValues-tmpBstar 

## End(Not run)

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

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

RefFreeEWAS

EWAS using Reference-Free DNA Methylation Mixture Deconvolution

v2.2

GPL (>= 2)

Authors

E. Andres Houseman, Sc.D.

Initial release

2018-12-14