Difference between revisions of "RAREFY DOCUMENTATION"
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==SOFTWARE INTERFACE== | ==SOFTWARE INTERFACE== | ||
| − | + | Options: | |
| − | + | Input Files : --ped [], --dat [] | |
Methods : --MCMC, --traitIncreasing, --traitDecreasing | Methods : --MCMC, --traitIncreasing, --traitDecreasing | ||
| − | + | Trait : --inverseNormal, --logTransform, --useCovariates, | |
--traitName [] | --traitName [] | ||
| − | + | Parameters : --maf [1.0e-03], --effect [2.00] | |
MCMC : --seed, --chains [3], --iterations [50000000] | MCMC : --seed, --chains [3], --iterations [50000000] | ||
| − | + | Other : --famList [], --famID [], --cpus [5], --prefix [] | |
==EXAMPLES== | ==EXAMPLES== | ||
Revision as of 15:13, 3 February 2015
KEY FEATURES
- RAREFY is a likelihood-based method to prioritize individuals in family samples and population samples.
- RAREFY takes account familial relatedness and allows adjusting covariates.
- RAREFY is able to handle large and complex pedigrees.
INPUT FILE FORMAT
- RAREFY takes 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.
SOFTWARE INTERFACE
Options:
Input Files : --ped [], --dat []
Methods : --MCMC, --traitIncreasing, --traitDecreasing
Trait : --inverseNormal, --logTransform, --useCovariates,
--traitName []
Parameters : --maf [1.0e-03], --effect [2.00]
MCMC : --seed, --chains [3], --iterations [50000000]
Other : --famList [], --famID [], --cpus [5], --prefix []
