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, 05:08, 17 February 2015
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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== |
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| *'''RAREFY''' is able to handle large and complex pedigrees. | | *'''RAREFY''' is able to handle large and complex pedigrees. |
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− | ==WHERE TO DOWNLOAD== | + | ==DOWNLOAD & BUILD== |
| Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables. | | Please go to [[RAREFY_DOWNLOAD | '''DOWNLOAD PAGE''']] for source code and executables. |
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| *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. |
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− | ==OUTPUT FORMAT=== | + | ==OUTPUT FORMAT== |
| '''RAREFY''' generates output file with eight columns. | | '''RAREFY''' generates output file with eight columns. |
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| *To inverse Normalize the phenotype before analysis: | | *To inverse Normalize the phenotype before analysis: |
| rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --inverseNormal --prefix your.output.prefix | | 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: | | *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 | | rarefy --ped your.ped --dat your.dat --traitIncreasing --traitDecreasing --famList your.file.with.famID --prefix your.output.prefix |