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) 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) is similar to non-negative matrix factorization, with additional constraints and additional utilities.

Author
E. Andres Houseman, Sc.D.
Date of publication
2016-01-30 00:54:27
Maintainer
E. Andres Houseman <andres.houseman@oregonstate.edu>
License
GPL (>= 2)
Version
2.0

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

Files in this package

RefFreeEWAS
RefFreeEWAS/NAMESPACE
RefFreeEWAS/data
RefFreeEWAS/data/HNSCC.RData
RefFreeEWAS/data/RefFreeEWAS.RData
RefFreeEWAS/data/datalist
RefFreeEWAS/R
RefFreeEWAS/R/PairsBootRefFreeEwasModel.R
RefFreeEWAS/R/RefFreeCellMix.R
RefFreeEWAS/R/RefFreeEWAS.R
RefFreeEWAS/MD5
RefFreeEWAS/DESCRIPTION
RefFreeEWAS/man
RefFreeEWAS/man/deviance.RefFreeCellMix.Rd
RefFreeEWAS/man/RefFreeEwasModel.Rd
RefFreeEWAS/man/summary.BootRefFreeEwasModel.Rd
RefFreeEWAS/man/omnibusBoot.Rd
RefFreeEWAS/man/rfEwasExampleTRUEMethDMR.Rd
RefFreeEWAS/man/RefFreeCellMixArrayDevianceBoot.Rd
RefFreeEWAS/man/print.RefFreeCellMix.Rd
RefFreeEWAS/man/RefFreeCellMixArrayDevianceBoots.Rd
RefFreeEWAS/man/projectMix.Rd
RefFreeEWAS/man/RefFreeCellMixArray.Rd
RefFreeEWAS/man/Y.HNSCC.averageBetas.Rd
RefFreeEWAS/man/print.RefFreeEwasModel.Rd
RefFreeEWAS/man/X.HNSCC.caseStatusAge.Rd
RefFreeEWAS/man/rfEwasExampleBetaValues.Rd
RefFreeEWAS/man/RefFreeCellMix.Rd
RefFreeEWAS/man/BootOneRefFreeEwasModel.Rd
RefFreeEWAS/man/EstDimIC.Rd
RefFreeEWAS/man/rfEwasExampleTRUEAlpha.Rd
RefFreeEWAS/man/print.summaryBootRefFreeEwasModel.Rd
RefFreeEWAS/man/rfEwasExampleTRUEOmega.Rd
RefFreeEWAS/man/BootRefFreeEwasModel.Rd
RefFreeEWAS/man/PairsBootOneRefFreeEwasModel.Rd
RefFreeEWAS/man/summary.RefFreeCellMix.Rd
RefFreeEWAS/man/print.BootRefFreeEwasModel.Rd
RefFreeEWAS/man/RefFreeCellMixInitialize.Rd
RefFreeEWAS/man/rfEwasExampleTRUEBeta.Rd
RefFreeEWAS/man/svdSafe.Rd
RefFreeEWAS/man/bootstrapPairs.Rd
RefFreeEWAS/man/rfEwasExampleCovariate.Rd
RefFreeEWAS/man/PairsBootRefFreeEwasModel.Rd