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* --makeResiduals can be combined with --useCovariates to generate residuals from a simple linear regressions before analysis. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model.
* --makeResiduals can be combined with --useCovariates to generate residuals from a simple linear regressions before analysis. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model.
** An example Command line requesting pre-adjustment for covariates before fitting a variance component follows:
** An example Command line requesting pre-adjustment for covariates before fitting a variance component follows:
--makeResiduals --inverseNorma
* If --inverseNormal is used WITHOUT --makeResiduals, then trait values are inverse normalized before any model fitting.
* If --inverseNormal is used WITHOUT --makeResiduals, then trait values are inverse normalized before any model fitting.
* --traitName is created for situations when you have many traits saved in your PED and DAT file, but you are interested in one or a few of them. It can read a file ending with .txt with each trait of interest in a separate line, or trait names separated with "/". An example to handle one trait or multiple traits is in the following:
* --traitName is created for situations when you have many traits saved in your PED and DAT file, but you are interested in one or a few of them. It can read a file ending with .txt with each trait of interest in a separate line, or trait names separated with "/". An example to handle one trait or multiple traits is in the following:
