RAREFY DOCUMENTATION - Revision history

Shuang Feng: /* Useful Wiki Pages */

2015-02-17T09:08:59Z

Useful Wiki Pages

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	* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
	* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]		* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]
			* The [[RAREFY_TUTORIAL \| '''RAREFY Tutorial''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]

2015-02-17T07:41:40Z

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			== Useful Wiki Pages ==

			* The [[RAREFY \| '''RAREFY Home''']]
			* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
			* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]
			* The [[RAREFY_FAQ \| '''FAQ''']]

	==KEY FEATURES==		==KEY FEATURES==

2015-02-17T00:05:18Z

DOWNLOAD and BUILD

← Older revision		Revision as of 20:05, 16 February 2015
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	*'''RAREFY''' is able to handle large and complex pedigrees.		*'''RAREFY''' is able to handle large and complex pedigrees.

	==DOWNLOAD ~~and~~ BUILD==		==DOWNLOAD & BUILD==
	Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.		Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.

2015-02-17T00:05:08Z

← Older revision		Revision as of 20:05, 16 February 2015
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	*'''RAREFY''' is able to handle large and complex pedigrees.		*'''RAREFY''' is able to handle large and complex pedigrees.

	==~~WHERE TO~~ DOWNLOAD==		==DOWNLOAD and BUILD==
	Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.		Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.

2015-02-16T23:37:12Z

EXAMPLES

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	*To inverse Normalize the phenotype before analysis:		*To inverse Normalize the phenotype before analysis:
	rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix		rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix
			*To inverse Normalize the phenotype and then adjust covariates saved in PED/DAT file before RAREFY analysis:
			rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --useCovariates --prefix your.output.prefix
	*To analyze only a subset of families in the sample:		*To analyze only a subset of families in the sample:
	rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix		rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix

2015-02-16T23:21:15Z

OUTPUT FORMAT=

← Older revision		Revision as of 19:21, 16 February 2015
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	*Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.		*Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.

	==OUTPUT FORMAT===		==OUTPUT FORMAT==
	'''RAREFY''' generates output file with eight columns.		'''RAREFY''' generates output file with eight columns.

2015-02-16T23:21:02Z

INPUT FILE FORMAT

← Older revision		Revision as of 19:21, 16 February 2015
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	Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.		Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.

	==INPUT ~~FILE~~ FORMAT==		==INPUT FORMAT==
	*'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED/DAT files] as input, no MAP file is needed.		*'''RAREFY''' takes [http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html MERLIN format PED/DAT files] as input, no MAP file is needed.
	*Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.		*Input files should have pedigree information, phenotype, and covariates information (if covariates are to be adjusted) saved.

			==OUTPUT FORMAT===
			'''RAREFY''' generates output file with eight columns.

	==SOFTWARE INTERFACE==		==SOFTWARE INTERFACE==

2015-02-16T23:19:39Z

← Older revision		Revision as of 19:19, 16 February 2015
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	*'''RAREFY''' is able to handle large and complex pedigrees.		*'''RAREFY''' is able to handle large and complex pedigrees.

			==WHERE TO DOWNLOAD==
			Please go to [[RAREFY_DOWNLOAD \| '''DOWNLOAD PAGE''']] for source code and executables.

	==INPUT FILE FORMAT==		==INPUT FILE FORMAT==

2015-02-16T23:18:05Z

EXAMPLES

← Older revision		Revision as of 19:18, 16 February 2015
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	rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famID fam123 --prefix your.output.prefix		rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famID fam123 --prefix your.output.prefix
	NOTE: although only the family included in --famID will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.		NOTE: although only the family included in --famID will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.
			*To analyze only one trait saved in your.ped and your.dat file:
			rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --traitName LDL --prefix your.output.prefix

2015-02-16T23:17:09Z

SOFTWARE INTERFACE

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	Other : --famList [], --famID [], --cpus [5], --prefix []		Other : --famList [], --famID [], --cpus [5], --prefix []

	Please see [[RAREFY_COMMAND\| RAREFY COMMAND]] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES \| EXAMPLES]] for quick examples.		Please see [[RAREFY_COMMAND\| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES \| '''EXAMPLES''']] for quick examples.

	==EXAMPLES==		==EXAMPLES==

← Older revision		Revision as of 05:08, 17 February 2015
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	* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]		* The [[RAREFY_DOWNLOAD \| '''RAREFY Download Page''']]
	* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]		* The [[RAREFY_COMMAND \| '''RAREFY Command Reference''']]
			* The [[RAREFY_TUTORIAL \| '''RAREFY Tutorial''']]
	* The [[RAREFY_FAQ \| '''FAQ''']]		* The [[RAREFY_FAQ \| '''FAQ''']]