Difference between revisions of "RAREFY DOCUMENTATION"

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(SOFTWARE INTERFACE)
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==KEY FEATURES==
 
==KEY FEATURES==
  
*'''RAREFY''' is a likelihood-based method to prioritize individuals in family samples and population samples.  
+
*'''RAREFY''' is a likelihood-based method to prioritize individuals in family AND population samples.  
  
 
*'''RAREFY''' takes account familial relatedness and allows adjusting covariates.
 
*'''RAREFY''' takes account familial relatedness and allows adjusting covariates.
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==EXAMPLES==
 
==EXAMPLES==
 +
*To prioritize individuals likely to be carriers of trait-increasing rare variants:
 +
rarefy --ped your.ped --dat your.dat --traitIncreasing --prefix your.output.prefix
 +
*To prioritize individuals likely to be carriers of trait-decreasing rare variants:
 +
rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix
 +
*To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants:
 +
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --prefix your.output.prefix
 +
*To analyze families using MCMC method in 3 chains and 50000000 iterations:
 +
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix
 +
*To inverse Normalize the phenotype before analysis:
 +
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --inverseNormal --prefix your.output.prefix
 +
*To analyze only a subset of families in the sample:
 +
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix
 +
*To analyze only one family:
 +
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famID fam123 --prefix your.output.prefix

Revision as of 19:04, 16 February 2015

KEY FEATURES

  • RAREFY is a likelihood-based method to prioritize individuals in family 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, --useCovariates, --traitName []
   Parameters : --maf [1.0e-03], --effect [1.00]
         MCMC : --seed, --chains [3], --iterations [50000000]
        Other : --famList [], --famID [], --cpus [5], --prefix []

EXAMPLES

  • To prioritize individuals likely to be carriers of trait-increasing rare variants:
rarefy --ped your.ped --dat your.dat --traitIncreasing --prefix your.output.prefix
  • To prioritize individuals likely to be carriers of trait-decreasing rare variants:
rarefy --ped your.ped --dat your.dat --traitDecreasing --prefix your.output.prefix
  • To prioritize individuals likely to be carriers of either trait-decreasing or trait-decreasing rare variants:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --prefix your.output.prefix
  • To analyze families using MCMC method in 3 chains and 50000000 iterations:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix
  • To inverse Normalize the phenotype before analysis:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --inverseNormal --prefix your.output.prefix 
  • To analyze only a subset of families in the sample:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix 
  • To analyze only one family:
rarefy --ped your.ped --dat your.dat --traitDecreasing --traitDecreasing --famID fam123 --prefix your.output.prefix