RAREFY COMMAND - Revision history

Shuang Feng: /* Useful Wiki Pages */

2015-02-17T09:09:11Z

Useful Wiki Pages

← Older revision		Revision as of 05:09, 17 February 2015
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	* The [[RAREFY \| '''RAREFY Home''']]		* The [[RAREFY \| '''RAREFY Home''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
			* The [[RAREFY_TUTORIAL \| '''RAREFY Tutorial''']]
	* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]

2015-02-17T07:40:42Z

--ped [string]

← Older revision		Revision as of 03:40, 17 February 2015
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	==Input Files==		==Input Files==
	===--ped [string]===		===--ped [string]===
	followed by the file name of your[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.		followed by the file name of your [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED] file.

	===--dat [string]===		===--dat [string]===

2015-02-17T07:40:32Z

Useful Wiki Pages

← Older revision		Revision as of 03:40, 17 February 2015
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	* The [[RAREFY \| '''RAREFY Home''']]		* The [[RAREFY \| '''RAREFY Home''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
	* The [[RAREFY_DOWNLOAD \| '''RAREFY ~~DOWNLOAD PAGE~~''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]

2015-02-17T07:40:16Z

Useful Wiki Pages

← Older revision		Revision as of 03:40, 17 February 2015
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	== Useful Wiki Pages ==		== Useful Wiki Pages ==

	* The [[RAREFY \| '''RAREFY ~~Homepage~~''']]		* The [[RAREFY \| '''RAREFY Home''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
	* The [[RAREFY_DOWNLOAD \| '''RAREFY DOWNLOAD PAGE''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY DOWNLOAD PAGE''']]

2015-02-17T07:40:03Z

← Older revision		Revision as of 03:40, 17 February 2015
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			== Useful Wiki Pages ==

			* The [[RAREFY \| '''RAREFY Homepage''']]
			* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
			* The [[RAREFY_DOWNLOAD \| '''RAREFY DOWNLOAD PAGE''']]
			* The [[RAREFY_FAQ \| '''FAQ''']]

			==RAREFY COMMANDS==
	Options:		Options:
	Input Files : --ped [], --dat []		Input Files : --ped [], --dat []

2015-02-17T00:10:29Z

MCMC

← Older revision		Revision as of 20:10, 16 February 2015
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	==MCMC==		==MCMC==
	===--seed [~~double~~]===		===--seed [int]===
	===--chains [int]===		===--chains [int]===
	The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains.		The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains.

2015-02-17T00:09:58Z

MCMC

← Older revision		Revision as of 20:09, 16 February 2015
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	===--seed [double]===		===--seed [double]===
	===--chains [int]===		===--chains [int]===
			The default is '''3'''. This options allows users to specify number of MCMC chains to run with different starting point. In general, less than 10 chains is recommended. The result is averaged over all chains.
	===--iterations [int]===		===--iterations [int]===
			The default is 50 million iterations. This option allows users to specify number of total iterations run in MCMC. Each chain will have the same amount of iterations divided from the total.

	==Others==		==Others==

2015-02-17T00:00:51Z

--cpus [int]

← Older revision		Revision as of 20:00, 16 February 2015
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	===--cpus [int]===		===--cpus [int]===
	This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.		This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.
	NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [[RAREFY_DOWNLOAD \| '''COMPILE''']] for more information.		NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer to [[RAREFY_DOWNLOAD \| '''COMPILE''']] for more information.

	===--prefix [string]===		===--prefix [string]===
	This option allows users to customize the output prefix generated by RAREFY.		This option allows users to customize the output prefix generated by RAREFY.

2015-02-17T00:00:39Z

--cpus [int]

← Older revision		Revision as of 20:00, 16 February 2015
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	===--cpus [int]===		===--cpus [int]===
	This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.		This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.
	NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [RAREFY_DOWNLOAD \| '''COMPILE'''] for more information.		NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [[RAREFY_DOWNLOAD \| '''COMPILE''']] for more information.

	===--prefix [string]===		===--prefix [string]===
	This option allows users to customize the output prefix generated by RAREFY.		This option allows users to customize the output prefix generated by RAREFY.

2015-02-17T00:00:26Z

--cpus [int]

← Older revision		Revision as of 20:00, 16 February 2015
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	This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.		This option allows analysis of only a single family. However, all families included in PED/DAT file will be used to fit variance component model.
	===--cpus [int]===		===--cpus [int]===
	This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.		This option allows parallel computing using multiple CPUs. However, the maximum number of CPUs used is capped by number of chains specified in --chains option, if MCMC method is used.
			NOTE: a version of RAREFY allowing parallel computing must be compiled to use this option. Please refer [RAREFY_DOWNLOAD \| '''COMPILE'''] for more information.

	===--prefix [string]===		===--prefix [string]===
	This option allows users to customize the output prefix generated by RAREFY.		This option allows users to customize the output prefix generated by RAREFY.

← Older revision		Revision as of 05:09, 17 February 2015
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	* The [[RAREFY \| '''RAREFY Home''']]		* The [[RAREFY \| '''RAREFY Home''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
			* The [[RAREFY_TUTORIAL \| '''RAREFY Tutorial''']]
	* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]

← Older revision		Revision as of 03:40, 17 February 2015
Line 3:		Line 3:
	* The [[RAREFY \| '''RAREFY Home''']]		* The [[RAREFY \| '''RAREFY Home''']]
	* The [[RAREFY_DOC \| '''RAREFY Documentation''']]		* The [[RAREFY_DOC \| '''RAREFY Documentation''']]
	* The [[RAREFY_DOWNLOAD \| '''RAREFY ~~DOWNLOAD PAGE~~''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]