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RAREFY COMMAND

47 bytes removed, 19:53, 16 February 2015
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default is '''OFF''', but will be automatically turned on for families larger than 25 individuals.
===--traitIncreasing===[ON|OFF]: ===default is '''OFF'''; can be used together with '''--traitDecreasing''' options or used alone.===--traitDecreasing=== [ON|OFF]: === default is '''OFF'''; can be used together with '''--traitIncreasing''' options or used alone.
==Trait==
===--inverseNormal===[ON|OFF]: ===default is '''OFF'''; '''ON''' will inverse normalize (quantile normalize) traits before fitting variance component model or adjusting covariates (if requested by --useCovariates option). ===--useCovariates===[ON|OFF]: ===default is '''OFF'''; '''ON''' will adjust any covariates saved in PED/DAT file (covariates are labeled with "C" in DAT file). ===--traitName[string]===[your.trait.name.in.string]: default is to analyze all traits saved in PED/DAT file (traits are labeled with "T" in DAT file).
==Parameters==
===--maf[double]===[your.preferred.frequency.value]:default is '''0.001'''; this option let you change the value of the fixed prior frequency of a trait-associated variant of interest.
===--effect[double]===[your.preferred.effect.size]:default is '''1 SD'''; this option let you change the value of the fixed prior effect size of a trait-associated variant of interest.
==MCMC==
===--seed[double]======--chains[int]======--iterations[int]===
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