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, 19:04, 16 February 2015
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| ==KEY FEATURES== | | ==KEY FEATURES== |
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− | *'''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. |
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| *'''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 |