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