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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 |
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| == Obtaining EPACTS == | | == Obtaining EPACTS == |
| | | |
− | * The official release of EPACTS software is available at /net/csgsites/csg-old/kang/epacts/download/ . | + | * 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. |
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| | Firth Bias-Corrected Logistic Likelihood Ratio Test | | | Firth Bias-Corrected Logistic Likelihood Ratio Test |
| | Clement Ma | | | Clement Ma |
| + | |- |
| + | | b.spa2 |
| + | | Binary |
| + | | YES <br> |
| + | | Moderate |
| + | | Saddlepoint Approximation Method |
| + | | Shawn Lee & Rounak Dey |
| |- | | |- |
| | b.lrt | | | b.lrt |
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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 |
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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)
| + | $ 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://www.sph.umich.edu/csg/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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| 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 |
| | | |
| == 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. |