1 Introduction

The epigenomics road map describes locations of epigenetic marks in DNA from a variety of cell types. Of interest are locations of histone modifications, sites of DNA methylation, and regions of accessible chromatin.

This package presents a selection of elements of the road map including metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.

2 Metadata on the ChromImpute archive

2.1 Sample metadata

I have retrieved a Google Docs spreadsheet with comprehensive information. The mapmeta() function provides access to a local DataFrame image of the file as retrieved in mid April 2015. We provide a dynamic view of a selection of columns. Use the search box to filter records shown, for example .

meta = mapmeta()
## NOTE: input data had non-ASCII characters replaced by ' '.
kpc = c("Comments", "Epigenome.ID..EID.", "Epigenome.Mnemonic", "Quality.Rating", 
"", "ANATOMY", "TYPE")

2.2 Metadata on the inferred states

The chromatin states and standard colorings used are enumerated in states_25:


The emission parameters of the 25 state model are depicted in the supplementary Figure 33 of Ernst and Kellis:

im = readPNG(system.file("pngs/emparms.png", package="erma"))