EWAS using Reference-Free DNA Methylation Mixture Deconvolution

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Documentation for package ‘RefFreeEWAS’ version 2.2

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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
EstDimRMT Dimension estimation by Random Matrix Theory
ImputeByMean Simple imputation method based on row-mean
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
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
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
SVDwithMissing SVD with missing values
X.HNSCC.caseStatusAge HNSCC Example - Covariates
Y.HNSCC.averageBetas HNSCC Example - DNA Methylation Average Betas