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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_TUTORIAL | '''RAREFY Tutorial''']]
* The [[RAREFY_FAQ | '''FAQ''']]
==KEY FEATURES==
==KEY FEATURES==
*'''RAREFY''' is able to handle large and complex pedigrees.
*'''RAREFY''' is able to handle large and complex pedigrees.
==INPUT FILE FORMAT==
==DOWNLOAD & BUILD==
Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables.
==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==
Other : --famList [], --famID [], --cpus [5], --prefix []
Other : --famList [], --famID [], --cpus [5], --prefix []
Please see [RAREFY_COMMAND] for detailed description of usage, and [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==
*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
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
