Chromatin segmentation in R. For a full description and for citing us, see the following article on Genome Biology:
A Mammana, HR Chung (2015). Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome. Genome Biology 2015, 16:151
For using EpiCSeg from the command line, you can find the full manual HERE!
epicseg needs R 3.2 (or newer) and depends on Bioconductor packages, CRAN packages, and another package from github.
For the installation, most of the work is done by the function
devtools::install_github. Because lately this function cannot resolve Bioconductor dependencies anymore (see this issue: https://github.com/hadley/devtools/issues/700), we will need to install some Bioconductor packages manually.
The Bioconductor dependencies are
edgeR. At the interactive R terminal, type:
source("http://bioconductor.org/biocLite.R") biocLite(c("IRanges", "GenomicRanges", "bamsignals", "edgeR"))
Install and load the
devtools package to be able to directly install R packages hosted on github :
Usage from the command line
To use EpiCSeg from the command line, you need to:
- create a launcher to be used with Rscript. This is done
epicseg:::getLauncher("epicseg.R")at the R interactive terminal, which will create the file
epicseg.Rin your working directory. You can move and rename this file the way you want.
- To use it, type
Rscript epicseg.R subprogram arguments. In UNIX you can also simply do
./epicseg.R subprogram argumentsprovided that you have execution permission on the file
- To see what the available subprograms are, simply type:
- To see which arguments each subprogram needs, you can type:
Rscript epicseg.R subprogram