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, 05:10, 17 February 2015
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| * The [[RAREFY | '''RAREFY Homepage''']] | | * The [[RAREFY | '''RAREFY Homepage''']] |
| * The [[RAREFY_DOC | '''RAREFY Documentation''']] | | * The [[RAREFY_DOC | '''RAREFY Documentation''']] |
− | * The [[RAREFY_COMMAND | '''RAREFY COMMAND REFERENCE''']] | + | * The [[RAREFY_COMMAND | '''RAREFY Command Reference''']] |
| + | * The [[RAREFY_DOWNLOAD | '''RAREFY Download''']] |
| * The [[RAREFY_FAQ | '''FAQ''']] | | * The [[RAREFY_FAQ | '''FAQ''']] |
| | | |
| ==EXAMPLE DATA SET== | | ==EXAMPLE DATA SET== |
− | *Please download the [[rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory. | + | *Please download the [[Media:Rarefy.example.tar.gz | '''EXAMPLE''']] file to your directory. |
| + | *In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability. |
| + | *A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing. |
| | | |
| ==COMMAND== | | ==COMMAND== |
| + | *Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both. |
| + | rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1 |
| | | |
| ==OUTPUT== | | ==OUTPUT== |
| + | *Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in "sim1_simul_rarefy.trait.Decreasing.result" and "sim1_simul_rarefy.trait.Increasing.result" separately. |
| + | *Use the following command to sort the RAREFY score to select informative individuals: |
| + | sort -k7 -gr sim1_simul_rarefy.trait.Increasing.result | head -10 |
| + | *The top 10 selected individuals are: |
| + | famid pid fatid motid sex residual rarefy_idv_score rarefy_fam_score |
| + | 1994 5 1 2 1 4.05563 0.839037 2.73226 |
| + | 1994 2 0 0 2 3.66226 0.829384 2.73226 |
| + | 345 1 0 0 1 3.45514 0.785963 1.95526 |
| + | 345 4 1 2 2 3.20513 0.782924 1.95526 |
| + | 3503 4 1 2 2 3.33598 0.621358 1.85789 |
| + | 3503 1 0 0 1 2.15643 0.619741 1.85789 |
| + | 1994 3 1 2 1 2.25633 0.607197 2.73226 |
| + | 3503 5 1 2 1 2.51068 0.601241 1.85789 |
| + | 1994 4 1 2 2 1.85392 0.437127 2.73226 |
| + | 3860 2 0 0 2 2.45598 0.405228 1.5474 |