RefFreeEWAS (version 2.2)

RefFreeEwasModel: Reference-Free EWAS Model

Description

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

Usage

RefFreeEwasModel(Y, X, K, smallOutput=FALSE)

Arguments

Y

Matrix of DNA methylation beta values (CpGs x subjects). Missing values *are* supported.

X

Design matrix (subjects x covariates).

K

Latent variable dimension (d in Houseman et al., 2013, technical report)

smallOutput

Smaller output? (Should be FALSE if you intend to run bootstraps.)

Value

A list object of class “RefFreeEwasModel”. The most important elements are Beta and Bstar.

Details

Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. This method is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption. Returns mixture-adjusted Beta and unadjusted Bstar, as well as estimates of various latent quantities.

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

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)

# }