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| eFORGE is the epigenetic equivalent of the FORGE tool. For details of the FORGE analysis approach see documentation in the FORGE web version at | |
| http://www.1000genomes.org/forge-analysis | |
| 1. The script itself is currently called eforge.pl written in Perl. It has | |
| the following Perl dependencies. | |
| use 5.012; | |
| use warnings; | |
| use DBI; | |
| use Sort::Naturally; | |
| use Cwd; | |
| use Storable; | |
| use Getopt::Long; | |
| 2. The sqlite3 db file that stores the bitstrings. This file is called eforge.db currently. | |
| 3. A stored hash containing the parameters for the background selection. | |
| Currently one file with the 450k annotation data (mvp_bins). | |
| Both the database and the hash are downloadable from: | |
| http://eforge.cs.ucl.ac.uk/?download | |
| 4. an eforge.ini file in the same directory as the script. Edit this to provide the | |
| directory in which the database and hash are stored. | |
| 5. An R 3.0 installation with the "devtools" and "rCharts" packages installed. See | |
| https://github.com/ramnathv/rCharts. You will need to install the latest version e.g. | |
| require(devtools) | |
| install_github('rCharts', 'ramnathv', ref = "dev") | |
| The input data is one of several options. | |
| a. A list of 450k probeids (DMPs) | |
| b. BED format (for 450k probes) | |
| The analysis requires a minimum of 5 DMPs (this is not a strict limit but | |
| operationally is best). | |
| To work DMPs currently have to be on the 450k array. The script gives warnings | |
| on DMPs not found. | |
| It also warns for background sets that do not have the right number of probes | |
| chosen, but this is really for information only. | |
| It takes a series of command line options as follows | |
| -f : the file to run on | |
| -data : whether to analyse ENCODE (encode) or Epigenome Roadmap (erc) data | |
| -label : a name for the files that are generated and for the plot titles | |
| where there is a title. | |
| -format : for the input data format. If this is location data e.g. | |
| bed format, the probeid is obtained from | |
| the sqlite3 database. | |
| Some of these default as described in the perldoc. Minimally the command | |
| line is: | |
| eforge.pl -f probeidfile -label Some_label | |
| which will by default run on Epigenome Roadmap data | |
| OUTPUT | |
| ====== | |
| there are several outputs generated | |
| 1. A pdf static chart, that would be good for download. | |
| 2. A d3 interactive chart. | |
| 3. A Datatables table. | |
| 4. R code files for generating the charts and the table. | |
| 5. There's also a tsv file of the results. |