EPACTS - Revision history

Hmkang: /* Output Files */

2019-02-19T12:03:06Z

Output Files

← Older revision		Revision as of 12:03, 19 February 2019
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	# How can I read the EMMAX kinship file from produced from EPACTS?		# How can I read the EMMAX kinship file from produced from EPACTS?
	# * You can run the following command to dump your kinship matrix into a human-readable text format.		# * You can run the following command to dump your kinship matrix into a human-readable text format.
	$(EPACTS_DIR)~~/bin/epacts~~/bin/pEmmax kin-util --kinf [input.kinf] --outf [output.prefix] --dump		$(EPACTS_DIR)/bin/pEmmax kin-util --kinf [input.kinf] --outf [output.prefix] --dump

	=== More questions ===		=== More questions ===

Hmkang: /* Single Variant Tests */

2017-06-01T19:24:40Z

Single Variant Tests

← Older revision		Revision as of 19:24, 1 June 2017
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	\| Clement Ma		\| Clement Ma
	\|-		\|-
	\| b.~~spa~~		\| b.spa2
	\| Binary		\| Binary
	\| YES <br>		\| YES <br>

Hmkang: /* Currently Supported Statistical Tests */

2017-02-28T11:50:11Z

Currently Supported Statistical Tests

← Older revision		Revision as of 11:50, 28 February 2017
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	\| Linear Wald Test		\| Linear Wald Test
	\| Hyun Min Kang <br> (as implemented in lm in R)		\| Hyun Min Kang <br> (as implemented in lm in R)
	\|-
	~~\| q.score~~
	~~\| Quantitative~~
	~~\| YES <br> (Regressed Out)~~
	~~\| Fast~~
	~~\| Quantitative Score Test <br> (from Lin DY and Tang ZZ, AJHG 2011 89:354-67)~~
	~~\| Clement Ma~~
	\|-		\|-
	\| q.linear		\| q.linear

Hmkang: /* Installation Details */

2016-12-15T22:50:03Z

Installation Details

← Older revision		Revision as of 22:50, 15 December 2016
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	In order to use EPACTS in the CSG cluster, you do not need to install them. You can directly use or make a copy of the in-house release version at		In order to use EPACTS in the CSG cluster, you do not need to install them. You can directly use or make a copy of the in-house release version at

	/net/fantasia/home/hmkang/bin/epacts/		/net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts/

	* If you want to access previous versions, visit http://csg-old.sph.umich.edu/kang/epacts/download		* If you want to access previous versions, visit http://csg-old.sph.umich.edu/kang/epacts/download

Hmkang: /* Getting Started With Examples */

2016-12-15T22:48:50Z

Getting Started With Examples

← Older revision		Revision as of 22:48, 15 December 2016
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	== Getting Started With Examples ==		== Getting Started With Examples ==
	If you are using EPACTS from the CSG cluster, please set the following environment variable		If you are using EPACTS from the CSG cluster, please set the following environment variable
	EPACTS_DIR=/net/fantasia/home/hmkang/bin/epacts (in bash)		EPACTS_DIR=/net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts (in bash)
	setenv EPACTS_DIR /net/fantasia/home/hmkang/bin/epacts (in csh)		setenv EPACTS_DIR /net/fantasia/home/hmkang/tools/epacts-3.3.0/bin/epacts (in csh)

	If you downloaded EPACTS binary and please set EPACTS_DIR to the full path of the downloaded and uncompressed directory.		If you downloaded EPACTS binary and please set EPACTS_DIR to the full path of the downloaded and uncompressed directory.

Hmkang: /* Obtaining EPACTS */

2016-12-15T22:47:50Z

Obtaining EPACTS

← Older revision		Revision as of 22:47, 15 December 2016
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	== Obtaining EPACTS ==		== Obtaining EPACTS ==

	* The official release of EPACTS software is available at ~~http~~://~~csg-old~~.~~sph.umich.edu~~/~~kang~~/~~epacts/download/index.html~~		* The official release of EPACTS software is available at https://github.com/statgen/EPACTS
	** From the CSG cluster, it is available at /net/fantasia/home/bin/epacts/		** From the CSG cluster, it is available at /net/fantasia/home/bin/epacts/
	* Note that R (version 2.10 or higher) and gnuplot (version 4.2 or higher) must be installed in order to run EPACTS correctly.		* Note that R (version 2.10 or higher) and gnuplot (version 4.2 or higher) must be installed in order to run EPACTS correctly.

Hmkang: /* Installation Details */

2016-12-15T22:47:16Z

Installation Details

← Older revision		Revision as of 22:47, 15 December 2016
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	If you want to use EPACTS in an Ubuntu platform, following the step below		If you want to use EPACTS in an Ubuntu platform, following the step below

	*Download EPACTS source distribution at http://~~csg-old.sph.umich~~.~~edu~~/~~kang/epacts/download~~/EPACTS-3.~~2.6.tar.gz (165MB)~~		$ git clone https://github.com/statgen/EPACTS.git
	*Uncompress EPACTS ~~package, and install the package using the following set of commands~~		$ cd EPACTS
	* Visit http:/~~/csg~~-~~old.sph.umich.edu~~/~~kang~~/~~epacts~~/~~download for checking previous versions~~		$ ./configure --prefix [/path/to/install]
			$ make
			$ make install

	~~tar xzvf EPACTS-3.2.6.tar.gz~~
	~~cd EPACTS-3.2.6~~
	~~./configure --prefix=/path/to/install~~
	~~make~~
	~~make install~~

	(Important Note: '''make sure to specify --prefix=/path/to/install''' to avoid installing to the default path /usr/local/, which you may not have the permission. /home/your_userid/epacts might be a good one, if you are not sure where to install)		(Important Note: '''make sure to specify --prefix=/path/to/install''' to avoid installing to the default path /usr/local/, which you may not have the permission. /home/your_userid/epacts might be a good one, if you are not sure where to install)
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	/net/fantasia/home/hmkang/bin/epacts/		/net/fantasia/home/hmkang/bin/epacts/

			* If you want to access previous versions, visit http://csg-old.sph.umich.edu/kang/epacts/download

	== Getting Started With Examples ==		== Getting Started With Examples ==

Hmkang: /* Single Variant Tests */

2016-12-15T22:45:32Z

Single Variant Tests

← Older revision		Revision as of 22:45, 15 December 2016
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	\| Firth Bias-Corrected Logistic Likelihood Ratio Test		\| Firth Bias-Corrected Logistic Likelihood Ratio Test
	\| Clement Ma		\| Clement Ma
			\|-
			\| b.spa
			\| Binary
			\| YES <br>
			\| Moderate
			\| Saddlepoint Approximation Method
			\| Shawn Lee & Rounak Dey
	\|-		\|-
	\| b.lrt		\| b.lrt

Hmkang: /* Lastest ChangeLog */

2016-12-15T22:44:26Z

Lastest ChangeLog

← Older revision		Revision as of 22:44, 15 December 2016
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	== Lastest ChangeLog ==		== Lastest ChangeLog ==
			* Dec 15th, 2016 : EPACTS v3.3.0 release (github)
			** Moved the repository into github
			** Some major fixes in handling large sample size (>18,000)
			** Other minor bug fixes
	* July 10th, 2014 : EPACTS v3.2.6 release		* July 10th, 2014 : EPACTS v3.2.6 release
	** Minor bug fix in epacts-make-kin		** Minor bug fix in epacts-make-kin

Ppwhite: /* Installation Details */

2016-11-30T15:14:55Z

Installation Details

← Older revision		Revision as of 15:14, 30 November 2016
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	If you want to use EPACTS in an Ubuntu platform, following the step below		If you want to use EPACTS in an Ubuntu platform, following the step below

	*Download EPACTS source distribution at http://~~www~~.sph.umich.edu~~/csg~~/kang/epacts/download/EPACTS-3.2.6.tar.gz (165MB)		*Download EPACTS source distribution at http://csg-old.sph.umich.edu/kang/epacts/download/EPACTS-3.2.6.tar.gz (165MB)
	*Uncompress EPACTS package, and install the package using the following set of commands		*Uncompress EPACTS package, and install the package using the following set of commands
	* Visit http://~~www~~.sph.umich.edu~~/csg~~/kang/epacts/download for checking previous versions		* Visit http://csg-old.sph.umich.edu/kang/epacts/download for checking previous versions

	tar xzvf EPACTS-3.2.6.tar.gz		tar xzvf EPACTS-3.2.6.tar.gz