RAREFY DOCUMENTATION: Difference between revisions

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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 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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*'''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==
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   Input Files : --ped [], --dat []
   Input Files : --ped [], --dat []
       Methods : --MCMC, --traitIncreasing, --traitDecreasing
       Methods : --MCMC, --traitIncreasing, --traitDecreasing
         Trait : --inverseNormal, --logTransform, --useCovariates,
         Trait : --inverseNormal, --useCovariates, --traitName []
                --traitName []
     Parameters : --maf [1.0e-03], --effect [1.00]
     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 []
Please see [[RAREFY_COMMAND| '''RAREFY COMMAND REFERENCE''']] for detailed description of usage, and [[RAREFY_DOC#EXAMPLES | '''EXAMPLES''']] for quick examples.


==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 --traitIncreasing --traitDecreasing --prefix your.output.prefix
*To analyze families using MCMC method in 3 chains and 50000000 iterations:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix
*To inverse Normalize the phenotype before analysis:
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:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix
NOTE: although only the subset of families will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.
*To analyze only one family:
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.
*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

Latest revision as of 05:08, 17 February 2015

Useful Wiki Pages

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.

DOWNLOAD & BUILD

Please go to DOWNLOAD PAGE for source code and executables.

INPUT 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.

OUTPUT FORMAT

RAREFY generates output file with eight columns.

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 []

Please see RAREFY COMMAND REFERENCE for detailed description of usage, and EXAMPLES for quick 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 --traitIncreasing --traitDecreasing --prefix your.output.prefix
  • To analyze families using MCMC method in 3 chains and 50000000 iterations:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --MCMC --chains 3 --iterations 50000000 --prefix your.output.prefix
  • To inverse Normalize the phenotype before analysis:
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:
rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix 
NOTE: although only the subset of families will be "RAREFIED", all samples saved in your.ped will be used to fit variance component model.
  • To analyze only one family:
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.
  • 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
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