charlesbreeze/eFORGE

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Oct 28, 2014 Create README.md
	1	eFORGE is the epigenetic equivalent of the FORGE tool. For details of the FORGE analysis approach see documentation in the FORGE web version at
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	3	http://www.1000genomes.org/forge-analysis
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	5	eFORGE is also available as a web tool at
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	7	http://eforge.cs.ucl.ac.uk/
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	9	1. The script itself is currently called eforge.pl written in Perl. It has
	10	the following Perl dependencies.
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	12	use 5.012;
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	13
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	14	use warnings;
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	16	use DBI;
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	17
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	18	use Sort::Naturally;
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	20	use Cwd;
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	22	use Storable;
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	24	use Getopt::Long;
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	26	2. The sqlite3 db file that stores the bitstrings. This file is called eforge_1.1.db currently.
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	28	3. A stored hash containing the parameters for the background selection.
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	29	Currently two files, one with the 27k and one with the 450k annotation data (mvp_bins).
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	31	The database and the hashes are downloadable from:
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	32	http://eforge.cs.ucl.ac.uk/?download
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	34	4. An eforge.ini file in the same directory as the script. Edit this to provide the
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	35	directory in which the database and hash are stored.
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	37	5. An R 3.0 installation with the "devtools" and "rCharts" packages installed. See
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	39	https://github.com/ramnathv/rCharts. You will need to install the latest version e.g.
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	41	require(devtools)
	42	install_github('rCharts', 'ramnathv', ref = "dev")
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	44	The input data is one of several options.
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	46	a. A list of 450k probeids (DMPs)
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	48	b. BED format (for 450k probes)
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	50	The analysis requires a minimum of 5 DMPs (this is not a strict limit but
	51	operationally is best).
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	53	To work DMPs currently have to be on either the 27k or the the 450k array. The
	54	script gives warnings on DMPs not found.
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	56	It also warns for background sets that do not have the right number of probes
	57	chosen, but this is really for information only.
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	59	It takes a series of command line options as follows
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	61	-f : the file to run on
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	63	-data : whether to analyse ENCODE (encode) or Epigenome Roadmap (erc) data
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	65	-label : a name for the files that are generated and for the plot titles
	66	where there is a title.
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	68	-format : for the input data format. If this is location data e.g.
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	69	bed format, the probeid is obtained from
	70	the sqlite3 database.
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	72	Some of these default as described in the perldoc. Minimally the command
	73	line is:
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	75	eforge.pl -f probeidfile -label Some_label
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	77	which will by default run on Epigenome Roadmap data
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	79	OUTPUT
	80	======
	81	there are several outputs generated
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	83	1. A pdf static chart, that would be good for download.
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	85	2. A d3 interactive chart.
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	87	3. A Datatables table.
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	89	4. R code files for generating the charts and the table.
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	91	5. There is also a tsv file of the results.
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	93	WEBSERVER
	94	=========
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	96	To install the web interface, please refer to the INSTALL document in the webserver folder.