Difference between revisions of "RAREFY DOCUMENTATION"

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(SOFTWARE INTERFACE)
(SOFTWARE INTERFACE)
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==SOFTWARE INTERFACE==
 
==SOFTWARE INTERFACE==
  
Options:
+
Options:
    Input Files : --ped [], --dat []
+
  Input Files : --ped [], --dat []
 
       Methods : --MCMC, --traitIncreasing, --traitDecreasing
 
       Methods : --MCMC, --traitIncreasing, --traitDecreasing
            Trait : --inverseNormal, --logTransform, --useCovariates,
+
        Trait : --inverseNormal, --logTransform, --useCovariates,
 
                 --traitName []
 
                 --traitName []
  Parameters : --maf [1.0e-03], --effect [2.00]
+
    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 []
+
        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 []

EXAMPLES