FEM: Identification of Functional Epigenetic Modules
Version 3.4.0

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.

AuthorAndrew E. Teschendorff and Zhen Yang
Bioconductor views DifferentialExpression DifferentialMethylation NetworkEnrichment SystemsBiology
Date of publicationNone
MaintainerZhen Yang <yangzhen@picb.ac.cn>
LicenseGPL (>=2)
Version3.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FEM")

Getting started

Package overview

Popular man pages

DoEpiMod: Identifies differential DNA methylation network hotspots.
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...
Toydata: Artificial data set.
See all...

All man pages Function index File listing

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.

Functions

DoEpiMod Man page Source code
DoExpMod Man page Source code
DoFEMbi Man page Source code
DoIntEpi450k Man page Source code
DoIntExp Man page Source code
DoIntFEM450k Man page Source code
FEM Man page
FEM-package Man page
FemModShow Man page Source code
GenStatM Man page Source code
GenStatMsp Man page Source code
GenStatR Man page Source code
Realdata Man page
Toydata Man page
probe450kfemanno Man page
probeEPICfemanno Man page

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
FEM documentation built on May 20, 2017, 9:19 p.m.

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