Difference between revisions of "RAREFY TUTORIAL"
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Revision as of 04:29, 17 February 2015
Useful Wiki Pages
EXAMPLE DATA SET
- Please download the 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.
- 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
- Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in "sim1_simul_rarefy.trait.Decreasing.result" and "sim1_simul_rarefy.trait.Decreasing.result" separately.