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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>​
how_to_run_pure_gblup.txt ยท Last modified: 2019/07/30 18:41 by dani