FEM (Functional Epigenetic Modules) algorithm
FEM can dentify interactome hotspots of differential promoter methylation and differential ex-pression, where an inverse association between promoter methylation and gene expression is assumed.A R package to identify interactome hotspots of differential promoter methylation and differential expression, where an inverse association between promoter methylation and gene expression is assumed1.
Citation
Jiao Y, Widschwendter M, Teschendorff AE. “A systems-level integrative framework for genomewide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control.” Bioinformatics 2014, doi: 10.1093/bioinformatics/btu316 (2014-05-02)
Jones A, Teschendorff AE, Li Q, Hayward JD, Kannan A, et al. (2013) Role of dna methylation and epigenetic silencing of hand2 in endometrial cancer development. PLoS Med 10:e1001551.
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("FEM")Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FEM")PDF : A R package to identify interactome hotspots of differential promoter methylation and differential expression, where an inverse association between promoter methylation and gene expression is assumed1.
PDF: Reference Manual