RefFreeEWAS (version 2.2)

PairsBootRefFreeEwasModel: Bootstrap for Reference-Free EWAS Model, Accounting for Paired Data

Description

Bootstrap procedure for reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. This version accounts for paired data (e.g. twin data)

Usage

PairsBootRefFreeEwasModel(mod, nboot, pairID)

Arguments

mod

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

nboot

Number of bootstrap samples to generate.

pairID

Pair IDs (one unique value per pair).

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. This paired version facilitates the estimation of robust standard errors to account for paired data (e.g. twin data) using a strategy similar to that employed by Generalized Estimating Equations (GEEs). Specifically, in bootstrapping the errors, the pairs are sampled rather than individual arrays. An error will be generated unless each cluster has exactly two members (i.e. exactly two observations correspond to the same unique ID given in pairID).

References

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

See Also

RefFreeEwasModel,BootRefFreeEwasModel

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)

# }