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how_to_run_pure_gblup [2019/06/07 00:40] yutaka |
how_to_run_pure_gblup [2019/07/30 18:41] dani [Procedure to run GBLUP] |
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- | where $\mathbf{y}$ is a vector of observations, $\mathbf{b}$ is a vector of fixed effects (typically a single $\mu$), $\mathbf{u}$ is a vector of additive genetic effects, $\mathbf{e}$ is a vector of residual effects. We assume $\mathrm{var}(\mathbf{y})=\mathrm{var}(\mathbf{u})+\mathrm{var}(\mathbf{e})=\mathbf{G}\sigma_{u}^{2}+\mathbf{R}\sigma_{e}^{2}$ where $\mathbf{G}$ is the genomic relationship matrix, $\mathbf{R}$ is a diagonal matrix (typically $\mathbf{I}$), $\sigma_{u}^{2}$ is the additive genetic variance, and $\sigma_{e}^{2}$ is the residual variance. The system of mixed model equations (MME) is shown as follows. | + | where $\mathbf{y}$ is a vector of observations, $\mathbf{X}$ is a design matrix relating the fixed effects to the observations (typically $\mathbf{1}$), $\mathbf{b}$ is a vector of fixed effects (typically a single $\mu$), $\mathbf{u}$ is a vector of additive genetic effects, $\mathbf{e}$ is a vector of residual effects. We assume $\mathrm{var}(\mathbf{y})=\mathrm{var}(\mathbf{u})+\mathrm{var}(\mathbf{e})=\mathbf{G}\sigma_{u}^{2}+\mathbf{R}\sigma_{e}^{2}$ where $\mathbf{G}$ is the genomic relationship matrix, $\mathbf{R}$ is a diagonal matrix (typically $\mathbf{I}$), $\sigma_{u}^{2}$ is the additive genetic variance, and $\sigma_{e}^{2}$ is the residual variance. The system of mixed model equations (MME) is shown as follows. |
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\right] | \right] | ||
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- | Note that $\mathbf{R}^{-1}=\mathbf{I}/\sigma_{e}^{2}$. | + | Note that $\mathbf{R}^{-1}=\mathbf{I}/\sigma_{e}^{2}$ in the typical case. |
===== A way to build MME in blupf90 ===== | ===== A way to build MME in blupf90 ===== | ||
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The blupf90 program is designed to solve the animal model that has the inverse of the numerator relationship matrix ($\mathbf{A}^{-1}$). Also, this program is extended to perform the single-step GBLUP analysis including the inverse of a subset pedigree matrix for genotyped animals ($\mathbf{A}_{22}^{-1}$) as well as $\mathbf{G}^{-1}$. | The blupf90 program is designed to solve the animal model that has the inverse of the numerator relationship matrix ($\mathbf{A}^{-1}$). Also, this program is extended to perform the single-step GBLUP analysis including the inverse of a subset pedigree matrix for genotyped animals ($\mathbf{A}_{22}^{-1}$) as well as $\mathbf{G}^{-1}$. | ||
- | Regardless of the above GBLUP model, the program literally creates the following MME. | + | Regardless of whether you need the pedigree relationships, the program literally creates the following MME. |
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1.00 | 1.00 | ||
OPTION AlphaBeta 1 0 | OPTION AlphaBeta 1 0 | ||
- | OPTION GammaDelta 0 0 | ||
OPTION tunedG 0 | OPTION tunedG 0 | ||
</file> | </file> |