EWAS using Reference-Free DNA Methylation Mixture Deconvolution

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Documentation for package ‘RefFreeEWAS’ version 2.2

• DESCRIPTION file.

Help Pages

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