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RefFreeEWAS (version 1.01)

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

1.01

License

GPL (>= 2)

Maintainer

E Andres Houseman

Last Published

December 4th, 2013

Functions in RefFreeEWAS (1.01)

EstDimIC

Dimension estimation by AIC and BIC
BootRefFreeEwasModel

Bootstrap for Reference-Free EWAS Model
omnibusBoot

Bootstrap-based omnibus test of significance across all features
rfEwasExampleTRUEBeta

True beta coefficients used in simulation (for comparison purposes)
BootOneRefFreeEwasModel

One Bootstrap sample for Reference-Free EWAS Model
rfEwasExampleTRUEOmega

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

True alpha intercepts used in simulation
rfEwasExampleCovariate

Simulated covariate for mixed-cell DNA methylation data set
svdSafe

Safe SVD-like matrix decomposition
rfEwasExampleTRUEMethDMR

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

print.BootRefFreeEwasModel
print.summaryBootRefFreeEwasModel

print.summaryBootRefFreeEwasModel
summary.BootRefFreeEwasModel

summary.BootRefFreeEwasModel
RefFreeEwasModel

Reference-Free EWAS Model
rfEwasExampleBetaValues

Simulated mixed-cell DNA methylation data set
print.RefFreeEwasModel

print.RefFreeEwasModel