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RefFreeEWAS

EWAS using Reference-Free DNA Methylation Mixture Deconvolution

Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption. The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.

Functions (35)

BootOneRefFreeEwasModel

One Bootstrap sample for Reference-Free EWAS Model

BootRefFreeEwasModel

Bootstrap for Reference-Free EWAS Model

EstDimIC

Dimension estimation by AIC and BIC

EstDimRMT

Dimension estimation by Random Matrix Theory

ImputeByMean

Simple imputation method based on row-mean

PairsBootOneRefFreeEwasModel

One Bootstrap Sample for Reference-Free EWAS Model, Accounting for Paired Data

PairsBootRefFreeEwasModel

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

RefFreeCellMix

Reference-Free Cell Mixture Projection

RefFreeCellMixArray

Initialize Reference-Free Cell Mixture Projection

RefFreeCellMixArrayDevianceBoot

RefFreeCellMixArrayDevianceBoot

RefFreeCellMixArrayDevianceBoots

RefFreeCellMixArrayDevianceBoots

RefFreeCellMixArrayWithCustomStart

Reference-Free Cell Mixture Projection - Custom Initialization

RefFreeCellMixInitialize

Initialize Reference-Free Cell Mixture Projection

RefFreeCellMixInitializeBySVD

Initialize Reference-Free Cell Mixture Projection by SVD

RefFreeEwasModel

Reference-Free EWAS Model

SVDwithMissing

SVD with missing values

X.HNSCC.caseStatusAge

HNSCC Example - Covariates

Y.HNSCC.averageBetas

HNSCC Example - DNA Methylation Average Betas

bootstrapPairs

One Bootstrap Sample for Pairs

deviance.RefFreeCellMix

deviance.RefFreeCellMix

omnibusBoot

Bootstrap-based omnibus test of significance across all features

print.BootRefFreeEwasModel

print.BootRefFreeEwasModel

print.RefFreeCellMix

print.RefFreeCellMix

print.RefFreeEwasModel

print.RefFreeEwasModel

print.summaryBootRefFreeEwasModel

print.summaryBootRefFreeEwasModel

projectMix

Cell Mixture Projection (reference-based)

rfEwasExampleBetaValues

Simulated mixed-cell DNA methylation data set

rfEwasExampleCovariate

Simulated covariate for mixed-cell DNA methylation data set

rfEwasExampleTRUEAlpha

True alpha intercepts used in simulation

rfEwasExampleTRUEBeta

True beta coefficients used in simulation (for comparison purposes)

rfEwasExampleTRUEMethDMR

True M matrix (cell-specific methylation values) used in simulation (for comparison purposes)

rfEwasExampleTRUEOmega

True Omega (cell mixture) coefficients used in simulation (for comparison purposes)

summary.BootRefFreeEwasModel

summary.BootRefFreeEwasModel

summary.RefFreeCellMix

summary.RefFreeCellMix

svdSafe

Safe SVD-like matrix decomposition

RefFreeEWAS

EWAS using Reference-Free DNA Methylation Mixture Deconvolution

v2.2
GPL (>= 2)
Authors
E. Andres Houseman, Sc.D.
Initial release
2018-12-14

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