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.

Version: 2.1
Depends: R (≥ 3.2.2), isva, quadprog
Published: 2017-02-25
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman <eahouseman at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: RefFreeEWAS results


Reference manual: RefFreeEWAS.pdf
Package source: RefFreeEWAS_2.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X El Capitan binaries: r-release: not available
OS X Mavericks binaries: r-oldrel: RefFreeEWAS_2.1.tgz
Old sources: RefFreeEWAS archive


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