RefFreeEWAS

Package: RefFreeEWAS
Type: Package
Title: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Version: 2.0
Date: 2016-01-29
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman <andres.houseman@oregonstate.edu>
Depends: R (>= 3.2.2), isva, quadprog
Description:
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.
License: GPL (>= 2)
NeedsCompilation: no
Packaged: 2016-01-29 23:36:59 UTC; housemae
Repository: CRAN
Date/Publication: 2016-01-30 00:54:27

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'RefFreeEWAS' ...
** package 'RefFreeEWAS' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'RefFreeEWAS'
    finding HTML links ... done
    BootOneRefFreeEwasModel                 html  
    BootRefFreeEwasModel                    html  
    EstDimIC                                html  
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    PairsBootOneRefFreeEwasModel            html  
    PairsBootRefFreeEwasModel               html  
    RefFreeCellMix                          html  
    RefFreeCellMixArray                     html  
    RefFreeCellMixArrayDevianceBoot         html  
    RefFreeCellMixArrayDevianceBoots        html  
    RefFreeCellMixInitialize                html  
    RefFreeEwasModel                        html  
    X.HNSCC.caseStatusAge                   html  
    Y.HNSCC.averageBetas                    html  
    bootstrapPairs                          html  
    deviance.RefFreeCellMix                 html  
    omnibusBoot                             html  
    print.BootRefFreeEwasModel              html  
    print.RefFreeCellMix                    html  
    print.RefFreeEwasModel                  html  
    print.summaryBootRefFreeEwasModel       html  
    projectMix                              html  
    rfEwasExampleBetaValues                 html  
    rfEwasExampleCovariate                  html  
    rfEwasExampleTRUEAlpha                  html  
    rfEwasExampleTRUEBeta                   html  
    rfEwasExampleTRUEMethDMR                html  
    rfEwasExampleTRUEOmega                  html  
    summary.BootRefFreeEwasModel            html  
    summary.RefFreeCellMix                  html  
    svdSafe                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (RefFreeEWAS)
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