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.

Author
Andrew E. Teschendorff and Zhen Yang
Date of publication
None
Maintainer
Zhen Yang <yangzhen@picb.ac.cn>
License
GPL (>=2)
Version
3.2.0

View on Bioconductor

Man pages

DoEpiMod
Identifies differential DNA methylation network hotspots.
DoExpMod
Identifies differential mRNA expression network hotspots.
DoFEMbi
Identifies interactome hotspots of differential promoter DNAm...
DoIntEpi450k
Integrates statistics of differential DNA methylation for a...
DoIntExp
Integrates statistics of differential expression for a...
DoIntFEM450k
Integrates statistics of differential DNA methylation and...
FemModShow
Generates a figure showing the inferred FEM module(s)
FEM-package
Identification of interactome hotspots of differential...
GenStatM
Generation of differential DNA methylation statistics
GenStatMsp
Generation of differential DNA methylation statistics for...
GenStatR
Generation of differential expression statistics
probe450kfemanno
Processed annotation of Illumina 450k probes for use in the...
probeEPICfemanno
Processed annotation of Illumina EPIC probes for use in the...
Realdata
A dataset object derived from real DNA methylation and gene...
Toydata
Artificial data set.

Files in this package

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