readme.blupf90new
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
readme.blupf90new [2018/08/21 20:33] – shogo | readme.blupf90new [2022/05/03 23:26] – dani | ||
---|---|---|---|
Line 11: | Line 11: | ||
===== Options ===== | ===== Options ===== | ||
< | < | ||
- | OPTION method VCE (default BLUP) | + | OPTION method VCE (default BLUP with blupf90 options) |
</ | </ | ||
- | Run airemlf90 (default running blupf90) | + | Run airemlf90 |
< | < | ||
OPTION conv_crit 1d-12 | OPTION conv_crit 1d-12 | ||
Line 133: | Line 133: | ||
< | < | ||
Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) | Indicate to store in file samples of (co)variances function for postprocessing (histogram, etc.) | ||
+ | |||
+ | ==== Omit A-inverse ==== | ||
+ | |||
+ | OPTION omit_ainv | ||
+ | |||
+ | This option prohibits the program from creating $\mathbf{A}^{-1}$. | ||
+ | It is especially useful for GBLUP. | ||
+ | For example, if you would like to perform the exact GBLUP, you can put the following options to your parameter file. | ||
+ | |||
+ | OPTION omit_ainv | ||
+ | OPTION TauOmega 1.0 0.0 | ||
+ | OPTION AlphaBeta 0.95 0.05 | ||
+ | |||
+ | With the above options, the program doesn' | ||
+ | |||
+ | === Details === | ||
+ | Assuming a single-trait ssGBLUP, the mixed model equations are as follows. | ||
+ | |||
+ | \( | ||
+ | \left[ | ||
+ | \begin{array}{ll} | ||
+ | \mathbf{X}' | ||
+ | \mathbf{Z}' | ||
+ | \end{array} | ||
+ | \right] | ||
+ | \left[ | ||
+ | \begin{array}{c} | ||
+ | \mathbf{\hat{b}}\\ | ||
+ | \mathbf{\hat{u}} | ||
+ | \end{array} | ||
+ | \right] | ||
+ | = | ||
+ | \left[ | ||
+ | \begin{array}{c} | ||
+ | \mathbf{X}' | ||
+ | \mathbf{Z}' | ||
+ | \end{array} | ||
+ | \right] | ||
+ | \) | ||
+ | |||
+ | where $\mathbf{H}$ is a matrix combining additive genetic relationship matrices and a genomic relationship matrix. | ||
+ | |||
+ | \( | ||
+ | \mathbf{H}^{-1} | ||
+ | = | ||
+ | \mathbf{A}^{-1} | ||
+ | + | ||
+ | \left[ | ||
+ | \begin{array}{cc} | ||
+ | \mathbf{0} & \mathbf{0} \\ | ||
+ | \mathbf{0} & \tau\mathbf{G}^{-1}-\omega\mathbf{A}_{22}^{-1} | ||
+ | \end{array} | ||
+ | \right] | ||
+ | \) | ||
+ | |||
+ | If we omit $\mathbf{A}^{-1}$ and $\mathbf{A}_{22}^{-1}$, | ||
+ | GBLUP by BLUPF90 was not so easy because the program creates $\mathbf{A}^{-1}$ by default and there was no way to avoid this behavior. | ||
+ | The new option removes $\mathbf{A}^{-1}$ from the equations so GBLUP will be easily performed. | ||
+ | |||
+ | ===== Storing accuracy based on PEV ===== | ||
===== Tricks ===== | ===== Tricks ===== |