iEDGE

Integrative analysis of (Epi-)DNA and Gene Expression Data

iEDGE is an R-package for performing integrative analysis of (epi-)DNA and gene expression data that builds upon, and significantly expands, the methodology first described in Monti, Chapuy, et. al., Cancer Cell (2012). This package provides the generalized pipeline to perform integrative analysis of epi-genomic data (methylation, copy number alteration, mutation, microRNA, etc.) and gene-expression data from paired samples, and consists of 3 major modules:

1. cis/trans differential expression analysis of epi-DNA and gene expression data
2. pathway enrichment analysis of significant cis and trans genes associated with the epi-DNA alterations
3. pruning of cis/trans epi-DNA to gene expression connections using a statistical mediation model

Reporting options are available in table (.txt) format as well as in html format, supported by interactive plots and tables

Installing iEDGE

library(devtools)

install_github("montilab/iEDGE")

library(iEDGE)