# Identification of Functional Epigenetic Modules

## Documentation for package ‘FEM’ version 3.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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