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.
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 .
library(DT)
library(erma)
meta = mapmeta()## NOTE: input data had non-ASCII characters replaced by ' '.kpc = c("Comments", "Epigenome.ID..EID.", "Epigenome.Mnemonic", "Quality.Rating",
"Standardized.Epigenome.name", "ANATOMY", "TYPE")
datatable(as.data.frame(meta[,kpc]))The chromatin states and standard colorings
used are enumerated in states_25:
data(states_25)
datatable(states_25)The emission parameters of the 25 state model are depicted in the supplementary Figure 33 of Ernst and Kellis:
library(png)
im = readPNG(system.file("pngs/emparms.png", package="erma"))
grid.raster(im)