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== Lastest ChangeLog ==
== Lastest ChangeLog ==
* December 4th, 2012 : EPACTS v3.2.0 release
* February 28th, 2013 : EPACTS v3.2.0 release
** R package installation bug (for some users) was fixed
** R package installation bug (for some users) was fixed
** A bug in the MAF error for high frequency variants (AF>0.25) was now fixed
** A bug in the MAF error for high frequency variants (AF>0.25) was now fixed
** --bprange option is added to allow testing for small region size
** --bprange option is added to allow testing for small region size
** Additional minor bug fixes
** Additional minor bug fixes
See [[#Full ChangeLog]] for full details
== Key Features ==
== Key Features ==
# PVALUE : P-value from the test
# PVALUE : P-value from the test
# Additional columns specified by return values 'add'
# Additional columns specified by return values 'add'
== Full ChangeLog ==
* February 28th, 2013 : EPACTS v3.2.0 release
** R package installation bug (for some users) was fixed
** A bug in the MAF error for high frequency variants (AF>0.25) was now fixed
** SKAT version is updated to 0.81
** --bprange option is added to allow testing for small region size
** Additional minor bug fixes
* December 4th, 2012 : EPACTS v3.1.0 release
** Removed dependency on libR.so
** Additional minor bug fixes
** --bprange option is added to allow testing for small region size
** November 25th, 2012 : EPACTS v3.0.0 release
** Restructured with source code release (with autoconf / automake / libtools)
** Added zoom plot feature
** FRAC_BURDEN keyword was replace to FRAC_WITH_RARE for groupwise testing
* October 26th, 2012 : EPACTS v2.2.0-beta is released with the following updates
** Added --max-mac option
** Fixed Firth's bias-corrected test (by Clement Ma)
** Added more informative warning messages when index files do not exist
** Fixed the bug in the epacts-plot in plotting ties
** Fixed errors in the MAF estimates per case and control
** Fixed bug in --minRSQ option
* September 28, 2012 : EPACTS v2.11-beta is released with the following updates
** Counts and allele frequencies for case/control added for binary tests
** --max-maf parameter is added
** Fixed EMMAX error in MAF in the output
** More informative error messages
* September 27, 2012 : EPACTS v2.1-beta is released with the following updates
** EMMAX interface is changed. --kinOnly option is related with a new command '''make-kin'''
** SKAT-O is upgraded to version 0.77 with additional configurable parameter settings
** Some parameter names are renamed (e.g. --min-maf, --min-mac)
** Many minor bugs are fixed
* Jul 6, 2012 : EPACTS v2.01-beta is released with the following updates
** SKAT-O is upgraded to version 0.76
** Fixed minor bugs in option names (Thanks to Xueling Sim)
* Jul 3, 2012 : EPACTS v2.0-beta is released with the following updates
** Major restructuring of the software
** Annotation software is switched with built-in application
** Addition of SKAT-O and EMMAX burden test
** Minor bug fixes
* Apr 8, 2012 : EPACTS v1.2-alpha is released with the following updates, in addition to the following updates
** EMMAX bug in handling covariates was fixed
** Variable Threshold Test is added
** Variable Threshold Test with genomic score (e.g. GERP or PhyloP) is added.
* Apr 4, 2012 : EPACTS v1.1-alpha is released with the following updates, in addition to minor updates
** EMMAX burden test (Hyun Min Kang)
** Likelihood ratio test (Clement Ma)
** Updated version of Firth bias-corrected likelihood ratio test (Clement Ma)
** Updated version of EMMAX single variant test (Hyun Min Kang)
* Mar 29, 2012 : EPACTS v1.0-alpha is released
