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RAREFY DOCUMENTATION

1,264 bytes added, 19:04, 16 February 2015
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==KEY FEATURES==
*'''RAREFY''' is a likelihood-based method to prioritize individuals in family samples and AND population samples.
*'''RAREFY''' takes account familial relatedness and allows adjusting covariates.
==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
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