RefFreeEWAS: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Version 2.1

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.

Browse man pages Browse package API and functions Browse package files

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

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

Files

NAMESPACE
data
data/HNSCC.RData
data/RefFreeEWAS.RData
data/datalist
R
R/PairsBootRefFreeEwasModel.R
R/RefFreeCellMix.R
R/RefFreeEWAS.R
MD5
DESCRIPTION
man
man/deviance.RefFreeCellMix.Rd
man/RefFreeEwasModel.Rd
man/summary.BootRefFreeEwasModel.Rd
man/omnibusBoot.Rd
man/rfEwasExampleTRUEMethDMR.Rd
man/RefFreeCellMixArrayDevianceBoot.Rd
man/print.RefFreeCellMix.Rd
man/RefFreeCellMixArrayDevianceBoots.Rd
man/projectMix.Rd
man/RefFreeCellMixArray.Rd
man/Y.HNSCC.averageBetas.Rd
man/print.RefFreeEwasModel.Rd
man/X.HNSCC.caseStatusAge.Rd
man/rfEwasExampleBetaValues.Rd
man/RefFreeCellMix.Rd
man/BootOneRefFreeEwasModel.Rd
man/EstDimIC.Rd
man/rfEwasExampleTRUEAlpha.Rd
man/print.summaryBootRefFreeEwasModel.Rd
man/rfEwasExampleTRUEOmega.Rd
man/BootRefFreeEwasModel.Rd
man/PairsBootOneRefFreeEwasModel.Rd
man/summary.RefFreeCellMix.Rd
man/print.BootRefFreeEwasModel.Rd
man/RefFreeCellMixInitialize.Rd
man/rfEwasExampleTRUEBeta.Rd
man/svdSafe.Rd
man/bootstrapPairs.Rd
man/rfEwasExampleCovariate.Rd
man/PairsBootRefFreeEwasModel.Rd
RefFreeEWAS documentation built on May 19, 2017, 1:09 p.m.