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RefFreeEWAS (version 1.2)

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

1.2

License

GPL (>= 2)

Maintainer

E Andres Houseman

Last Published

March 5th, 2014

Functions in RefFreeEWAS (1.2)

summary.BootRefFreeEwasModel

summary.BootRefFreeEwasModel
EstDimIC

Dimension estimation by AIC and BIC
print.BootRefFreeEwasModel

print.BootRefFreeEwasModel
rfEwasExampleTRUEMethDMR

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

Reference-Free EWAS Model
BootRefFreeEwasModel

Bootstrap for Reference-Free EWAS Model
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
omnibusBoot

Bootstrap-based omnibus test of significance across all features
print.RefFreeEwasModel

print.RefFreeEwasModel
svdSafe

Safe SVD-like matrix decomposition
print.summaryBootRefFreeEwasModel

print.summaryBootRefFreeEwasModel
rfEwasExampleTRUEBeta

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

Simulated covariate for mixed-cell DNA methylation data set
rfEwasExampleBetaValues

Simulated mixed-cell DNA methylation data set