Difference between revisions of "RAREFY TUTORIAL"

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(EXAMPLE DATA SET)
(COMMAND)
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==COMMAND==
 
==COMMAND==
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*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.
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rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1
  
 
==OUTPUT==
 
==OUTPUT==

Revision as of 04:27, 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.

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