RefFreeEWAS: EWAS using Reference-Free DNA Methylation Mixture Deconvolution

Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption. The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.

Install the latest version of this package by entering the following in R:
install.packages("RefFreeEWAS")
AuthorE. Andres Houseman, Sc.D.
Date of publication2017-02-25 23:57:36
MaintainerE. Andres Houseman <eahouseman@gmail.com>
LicenseGPL (>= 2)
Version2.1

View on CRAN

Man 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

omnibusBoot: Bootstrap-based omnibus test of significance across all...

PairsBootOneRefFreeEwasModel: One Bootstrap Sample for Reference-Free EWAS Model,...

PairsBootRefFreeEwasModel: Bootstrap for Reference-Free EWAS Model, Accounting for...

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

RefFreeCellMixInitialize: Initialize Reference-Free Cell Mixture Projection

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...

rfEwasExampleTRUEMethDMR: True M matrix (cell-specific methylation values) used in...

rfEwasExampleTRUEOmega: True Omega (cell mixture) coefficients used in simulation...

summary.BootRefFreeEwasModel: summary.BootRefFreeEwasModel

summary.RefFreeCellMix: summary.RefFreeCellMix

svdSafe: Safe SVD-like matrix decomposition

X.HNSCC.caseStatusAge: HNSCC Example - Covariates

Y.HNSCC.averageBetas: HNSCC Example - DNA Methylation Average Betas

Functions

BootOneRefFreeEwasModel Man page
BootRefFreeEwasModel Man page
bootstrapPairs Man page
deviance.RefFreeCellMix Man page
EstDimIC Man page
omnibusBoot Man page
PairsBootOneRefFreeEwasModel Man page
PairsBootRefFreeEwasModel Man page
print.BootRefFreeEwasModel Man page
print.RefFreeCellMix Man page
print.RefFreeEwasModel Man page
print.summaryBootRefFreeEwasModel Man page
projectMix Man page
RefFreeCellMix Man page
RefFreeCellMixArray Man page
RefFreeCellMixArrayDevianceBoot Man page
RefFreeCellMixArrayDevianceBoots Man page
RefFreeCellMixInitialize Man page
RefFreeEwasModel Man page
rfEwasExampleBetaValues Man page
rfEwasExampleCovariate Man page
rfEwasExampleTRUEAlpha Man page
rfEwasExampleTRUEBeta Man page
rfEwasExampleTRUEMethDMR Man page
rfEwasExampleTRUEOmega Man page
summary.BootRefFreeEwasModel Man page
summary.RefFreeCellMix Man page
svdSafe Man page
X.HNSCC.caseStatusAge Man page
Y.HNSCC.averageBetas Man page

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