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FEM (version 2.8.0)

Identification of Functional Epigenetic Modules

Description

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.

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Version

Version

2.8.0

License

GPL (>=2)

Maintainer

Andrew E Teschendorff

Last Published

February 15th, 2017

Functions in FEM (2.8.0)

GenStatM

Generation of differential DNA methylation statistics
probe450kfemanno

Processed annotation of Illumina 450k probes for use in the FEM algorithm.
Toydata

Artificial data set.
DoIntFEM450k

Integrates statistics of differential DNA methylation and differential expression for a specified contrast with a network adjacency matrix.
DoEpiMod

Identifies differential DNA methylation network hotspots.
DoIntEpi450k

Integrates statistics of differential DNA methylation for a specified contrast with a network adjacency matrix.
DoExpMod

Identifies differential mRNA expression network hotspots.
DoFEMbi

Identifies interactome hotspots of differential promoter DNAm methylation and differential mRNA expression.
DoIntExp

Integrates statistics of differential expression for a specified contrast with a network adjacency matrix.
Realdata

A dataset object derived from real DNA methylation and gene expression data from normal endometrial and endometrial cancer tissue
GenStatR

Generation of differential expression statistics
FEM-package

Identification of interactome hotspots of differential promoter DNA methylation and differential expression
FemModShow

Generates a figure showing the inferred FEM module(s)