FEM: Identification of Functional Epigenetic Modules

The FEM package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FEM")
AuthorAndrew E. Teschendorff and Zhen Yang
Bioconductor views DifferentialExpression DifferentialMethylation NetworkEnrichment SystemsBiology
Date of publicationNone
MaintainerZhen Yang <yangzhen@picb.ac.cn>
LicenseGPL (>=2)
Version3.2.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/DoEpiMod.R R/DoExpMod.R R/DoFEMbi.R R/DoIntEpi450k.R R/DoIntExp.R R/DoIntFEM450k.R R/FemModShow.R R/GenStatM.R R/GenStatMsp.R R/GenStatR.R
build
build/vignette.rds
data
data/Realdata.rda
data/Toydata.rda
data/datalist
data/probe450kfemanno.rda
data/probeEPICfemanno.rda
inst
inst/CITATION
inst/doc
inst/doc/IntroDoFEM.R
inst/doc/IntroDoFEM.Rnw
inst/doc/IntroDoFEM.pdf
inst/unitTests
inst/unitTests/test_FEM.R
man
man/DoEpiMod.Rd man/DoExpMod.Rd man/DoFEMbi.Rd man/DoIntEpi450k.Rd man/DoIntExp.Rd man/DoIntFEM450k.Rd man/FEM-package.Rd man/FemModShow.Rd man/GenStatM.Rd man/GenStatMsp.Rd man/GenStatR.Rd man/Realdata.Rd man/Toydata.Rd man/probe450kfemanno.Rd man/probeEPICfemanno.Rd
tests
tests/runTests.R
vignettes
vignettes/HAND2.pdf
vignettes/HAND2epi.pdf
vignettes/IntroDoFEM.Rnw
vignettes/IntroDoFEM.bib
vignettes/ZWINTexp.pdf
vignettes/bmc_article.bst
vignettes/bmcart-biblio.sty
vignettes/cite.sty
vignettes/fancyvrb.sty
vignettes/inconsolata.sty
vignettes/lastpage.sty
vignettes/rotating.sty
vignettes/url.sty
vignettes/xcolor.sty

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