RareMETALS - Revision history

Dajiang Liu: /* Where to download */

2017-05-18T14:18:17Z

Where to download

← Older revision		Revision as of 10:18, 18 May 2017
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	== Where to download ==		== Where to download ==

	The R package can be downloaded from [[Media:rareMETALS_6.3.tar.gz \| rareMETALS_6.3.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.		The R package can be downloaded from [[Media:rareMETALS_6.8.tar.gz \| rareMETALS_6.8.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.

	== Documentation ==		== Documentation ==

Dajiang Liu: /* Change Log */

2017-05-18T14:17:57Z

Change Log

← Older revision		Revision as of 10:17, 18 May 2017
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	== Change Log ==		== Change Log ==
			* 05/18/2017 Version 6.8 incorporates a number of new features and bug fixes. We included support for multi-allelic variants, the support for a new conditional analysis method, the support for cohort level genomic controls, and the bug fixes for calculating heterogeneity statistics such as Q and I2.
	* 04/09/2016 Version 6.3 is released. Minor bug fix: Due to different level of missingness of variants in the gene, the single variant association statistics calculated using the covariance matrices of score statistics can be different than single variant association statistics calculated using vstat. This has lead to confusions. It has been fixed in version 6.3. The primary results from version 6.2 should be correct.		* 04/09/2016 Version 6.3 is released. Minor bug fix: Due to different level of missingness of variants in the gene, the single variant association statistics calculated using the covariance matrices of score statistics can be different than single variant association statistics calculated using vstat. This has lead to confusions. It has been fixed in version 6.3. The primary results from version 6.2 should be correct.
	* 09/25/2015 Version 6.2 is released. Minor bug fix: Removed the incorrect warning information in version 6.1 when quantitative traits are meta-analyzed. The software incorrectly consider it as binary trait and suggested the use of rareMETALS2.		* 09/25/2015 Version 6.2 is released. Minor bug fix: Removed the incorrect warning information in version 6.1 when quantitative traits are meta-analyzed. The software incorrectly consider it as binary trait and suggested the use of rareMETALS2.

Dajiang Liu: /* Where to download */

2016-04-09T05:40:53Z

Where to download

← Older revision		Revision as of 01:40, 9 April 2016
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	== Where to download ==		== Where to download ==

	The R package can be downloaded from [[Media:rareMETALS_6.2.tar.gz \| rareMETALS_6.2.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.		The R package can be downloaded from [[Media:rareMETALS_6.3.tar.gz \| rareMETALS_6.3.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.

	== Documentation ==		== Documentation ==

Dajiang Liu: Undo revision 14146 by Dajiang Liu (talk)

2016-04-09T05:40:35Z

Undo revision 14146 by Dajiang Liu (talk)

← Older revision		Revision as of 01:40, 9 April 2016
Line 21:		Line 21:
	== Where to download ==		== Where to download ==

	The R package can be downloaded from [[Media:rareMETALS_6.3.tar.gz \| rareMETALS_6.3.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.		The R package can be downloaded from [[Media:rareMETALS_6.2.tar.gz \| rareMETALS_6.2.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.

	== Documentation ==		== Documentation ==

Dajiang Liu: /* Where to download */

2016-04-09T05:18:12Z

Where to download

← Older revision		Revision as of 01:18, 9 April 2016
Line 21:		Line 21:
	== Where to download ==		== Where to download ==

	The R package can be downloaded from [[Media:rareMETALS_6.2.tar.gz \| rareMETALS_6.2.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.		The R package can be downloaded from [[Media:rareMETALS_6.3.tar.gz \| rareMETALS_6.3.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.

	== Documentation ==		== Documentation ==

Dajiang Liu: /* Change Log */

2016-04-09T05:17:56Z

Change Log

← Older revision		Revision as of 01:17, 9 April 2016
Line 2:		Line 2:

	== Change Log ==		== Change Log ==
			* 04/09/2016 Version 6.3 is released. Minor bug fix: Due to different level of missingness of variants in the gene, the single variant association statistics calculated using the covariance matrices of score statistics can be different than single variant association statistics calculated using vstat. This has lead to confusions. It has been fixed in version 6.3. The primary results from version 6.2 should be correct.
	* 09/25/2015 Version 6.2 is released. Minor bug fix: Removed the incorrect warning information in version 6.1 when quantitative traits are meta-analyzed. The software incorrectly consider it as binary trait and suggested the use of rareMETALS2.		* 09/25/2015 Version 6.2 is released. Minor bug fix: Removed the incorrect warning information in version 6.1 when quantitative traits are meta-analyzed. The software incorrectly consider it as binary trait and suggested the use of rareMETALS2.
	* 07/23/2015 Version 6.1 is released. Minor feature changes include output for VT the sites where the statistics are maximized; fixed a bug for determining monomorphic sites. Issue warnings when rareMETALS is used to analyze binary trait for meta-analysis.		* 07/23/2015 Version 6.1 is released. Minor feature changes include output for VT the sites where the statistics are maximized; fixed a bug for determining monomorphic sites. Issue warnings when rareMETALS is used to analyze binary trait for meta-analysis.

Dajiang Liu: /* Where to download */

2015-09-26T03:27:13Z

Where to download

← Older revision		Revision as of 23:27, 25 September 2015
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	== Where to download ==		== Where to download ==

	The R package can be downloaded from [[Media:rareMETALS_6.1.tar.gz \| rareMETALS_6.1.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.		The R package can be downloaded from [[Media:rareMETALS_6.2.tar.gz \| rareMETALS_6.2.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.

	== Documentation ==		== Documentation ==

Dajiang Liu: /* Change Log */

2015-09-26T03:26:54Z

Change Log

← Older revision		Revision as of 23:26, 25 September 2015
Line 2:		Line 2:

	== Change Log ==		== Change Log ==
			* 09/25/2015 Version 6.2 is released. Minor bug fix: Removed the incorrect warning information in version 6.1 when quantitative traits are meta-analyzed. The software incorrectly consider it as binary trait and suggested the use of rareMETALS2.
	* 07/23/2015 Version 6.1 is released. Minor feature changes include output for VT the sites where the statistics are maximized; fixed a bug for determining monomorphic sites. Issue warnings when rareMETALS is used to analyze binary trait for meta-analysis.		* 07/23/2015 Version 6.1 is released. Minor feature changes include output for VT the sites where the statistics are maximized; fixed a bug for determining monomorphic sites. Issue warnings when rareMETALS is used to analyze binary trait for meta-analysis.
	* 05/19/2015 Version 6.0 is released. Minor feature addition: rareMETALS can now output of the set of variants that are analyzed in VT (i.e. the set of variants with MAF < the threshold where the VT statistic is maximized).		* 05/19/2015 Version 6.0 is released. Minor feature addition: rareMETALS can now output of the set of variants that are analyzed in VT (i.e. the set of variants with MAF < the threshold where the VT statistic is maximized).

Dajiang Liu: /* Where to download */

2015-07-25T20:08:12Z

Where to download

← Older revision		Revision as of 16:08, 25 July 2015
Line 19:		Line 19:
	== Where to download ==		== Where to download ==

	The R package can be downloaded from [[Media:rareMETALS_6.0.tar.gz \| rareMETALS_6.0.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.		The R package can be downloaded from [[Media:rareMETALS_6.1.tar.gz \| rareMETALS_6.1.tar.gz]]. It will be eventually released on the Comprehensive R-archive Network. If you want to perform gene-level association test using automatically generated annotations, you will also need [[Media:refFlat_hg19.txt.gz \| refFlat_hg19.txt.gz]], which is the gene definition modified from refFlat.

	== Documentation ==		== Documentation ==

Dajiang Liu: /* Change Log */

2015-07-25T20:07:58Z

Change Log

← Older revision		Revision as of 16:07, 25 July 2015
Line 2:		Line 2:

	== Change Log ==		== Change Log ==
			* 07/23/2015 Version 6.1 is released. Minor feature changes include output for VT the sites where the statistics are maximized; fixed a bug for determining monomorphic sites. Issue warnings when rareMETALS is used to analyze binary trait for meta-analysis.
	* 05/19/2015 Version 6.0 is released. Minor feature addition: rareMETALS can now output of the set of variants that are analyzed in VT (i.e. the set of variants with MAF < the threshold where the VT statistic is maximized).		* 05/19/2015 Version 6.0 is released. Minor feature addition: rareMETALS can now output of the set of variants that are analyzed in VT (i.e. the set of variants with MAF < the threshold where the VT statistic is maximized).
	* 04/01/2015 Version 5.9 is released (not a April's fool joke)! A bug in calculating Cochran-Q statistic is fixed. A bug in conditional.rareMETALS.range.group is also fixed. No other analyses are affected.		* 04/01/2015 Version 5.9 is released (not a April's fool joke)! A bug in calculating Cochran-Q statistic is fixed. A bug in conditional.rareMETALS.range.group is also fixed. No other analyses are affected.