# EWAS using Reference-Free DNA Methylation Mixture Deconvolution

## 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