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RefFreeEWAS (version 1.3)

EWAS using reference-Free DNA methylation mixture deconvolution

Description

Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. This method is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption.

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Version

Install

install.packages('RefFreeEWAS')

Monthly Downloads

37

Version

1.3

License

GPL (>= 2)

Maintainer

E Andres Houseman

Last Published

July 31st, 2014

Functions in RefFreeEWAS (1.3)

print.RefFreeEwasModel

print.RefFreeEwasModel
print.summaryBootRefFreeEwasModel

print.summaryBootRefFreeEwasModel
RefFreeEwasModel

Reference-Free EWAS Model
summary.BootRefFreeEwasModel

summary.BootRefFreeEwasModel
BootRefFreeEwasModel

Bootstrap for Reference-Free EWAS Model
EstDimIC

Dimension estimation by AIC and BIC
omnibusBoot

Bootstrap-based omnibus test of significance across all features
rfEwasExampleTRUEAlpha

True alpha intercepts used in simulation
rfEwasExampleTRUEMethDMR

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

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

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

True beta coefficients used in simulation (for comparison purposes)
print.BootRefFreeEwasModel

print.BootRefFreeEwasModel
svdSafe

Safe SVD-like matrix decomposition
BootOneRefFreeEwasModel

One Bootstrap sample for Reference-Free EWAS Model
bootstrapPairs

One Bootstrap Sample for Pairs
rfEwasExampleTRUEOmega

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

Simulated mixed-cell DNA methylation data set
rfEwasExampleCovariate

Simulated covariate for mixed-cell DNA methylation data set