EWAS using Reference-Free DNA Methylation Mixture Deconvolution

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Documentation for package ‘RefFreeEWAS’ version 2.1

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BootOneRefFreeEwasModel One Bootstrap sample for Reference-Free EWAS Model
BootRefFreeEwasModel Bootstrap for Reference-Free EWAS Model
bootstrapPairs One Bootstrap Sample for Pairs
deviance.RefFreeCellMix deviance.RefFreeCellMix
EstDimIC Dimension estimation by AIC and BIC
omnibusBoot Bootstrap-based omnibus test of significance across all features
PairsBootOneRefFreeEwasModel One Bootstrap Sample for Reference-Free EWAS Model, Accounting for Paired Data
PairsBootRefFreeEwasModel Bootstrap for Reference-Free EWAS Model, Accounting for Paired Data
print.BootRefFreeEwasModel print.BootRefFreeEwasModel
print.RefFreeCellMix print.RefFreeCellMix
print.RefFreeEwasModel print.RefFreeEwasModel
print.summaryBootRefFreeEwasModel print.summaryBootRefFreeEwasModel
projectMix Cell Mixture Projection (reference-based)
RefFreeCellMix Reference-Free Cell Mixture Projection
RefFreeCellMixArray Initialize Reference-Free Cell Mixture Projection
RefFreeCellMixArrayDevianceBoot RefFreeCellMixArrayDevianceBoot
RefFreeCellMixArrayDevianceBoots RefFreeCellMixArrayDevianceBoots
RefFreeCellMixInitialize Initialize Reference-Free Cell Mixture Projection
RefFreeEwasModel Reference-Free EWAS Model
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
X.HNSCC.caseStatusAge HNSCC Example - Covariates
Y.HNSCC.averageBetas HNSCC Example - DNA Methylation Average Betas