readme.blupf90
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readme.blupf90 [2012/05/28 14:34] – shogo | readme.blupf90 [2019/02/20 16:32] – andres | ||
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- | The documentation for blupf90 is available separately as a PDF document. | + | ====== BLUPF90 ====== |
- | The following lines can be added at the end of parameter file for blupf90: | + | |
- | Available options: | + | ===== Summary ===== |
+ | The documentation for blupf90 is available separately as a {{:blupf90.pdf|PDF}} document. | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
+ | ===== Options ===== | ||
+ | < | ||
OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
- | + | </ | |
- | Set convergence criteria (deault 1e-12). | + | Set convergence criteria (deault 1e-12). |
+ | < | ||
OPTION maxrounds 10000 | OPTION maxrounds 10000 | ||
- | + | </ | |
- | Set maximum number of rounds (default | + | Set maximum number of rounds (default |
+ | < | ||
OPTION solv_method FSPAK | OPTION solv_method FSPAK | ||
- | + | </ | |
- | Selection solutions by FSPAK, SOR or PCG (default PCG). | + | Selection solutions by FSPAK, SOR or PCG (default PCG). |
+ | < | ||
OPTION r_factor 1.6 | OPTION r_factor 1.6 | ||
+ | </ | ||
+ | Set relaxation factor for SOR (default 1.4). | ||
+ | < | ||
+ | OPTION sol se | ||
+ | </ | ||
+ | Store solutions and standard errors. | ||
+ | < | ||
+ | OPTION store_pev_pec 6 | ||
+ | </ | ||
+ | Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in " | ||
+ | < | ||
+ | OPTION missing -999 | ||
+ | </ | ||
+ | Specify missing observations (default 0) in integer. | ||
+ | < | ||
+ | OPTION residual | ||
+ | </ | ||
+ | y-hat and residual will be included in " | ||
+ | < | ||
+ | OPTION blksize 3 | ||
+ | </ | ||
+ | Set block size for preconditioner (default 1). | ||
+ | < | ||
+ | OPTION prior_solutions | ||
+ | </ | ||
+ | Using the previous solution file to start the iteration. An additional software is required to use this option. | ||
+ | < | ||
+ | OPTION stdresidual | ||
+ | </ | ||
+ | y-hat and student residuals will be included in " | ||
+ | < | ||
+ | OPTION check_levels 0 | ||
+ | </ | ||
+ | Check levels (default 1 = true). | ||
+ | < | ||
+ | OPTION use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. | ||
- | Set relaxation factor | + | < |
+ | OPTION snp_p_value | ||
+ | </ | ||
+ | Computes the elements of the inverse of the Mixed Model Equations that are needed | ||
- | OPTION sol se | + | ==== Omit A-inverse ==== |
- | | + | |
- | OPTION missing | + | 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 TauOmega 1.0 0.0 | ||
+ | OPTION AlphaBeta 0.95 0.05 | ||
- | OPTION residual | + | With the above options, the program doesn' |
- | y-hat and residual will be shown in yhat_residual. | + | === Details === |
+ | Assuming a single-trait ssGBLUP, the mixed model equations are as follows. | ||
- | OPTION blksize 3 | + | \( |
+ | \left[ | ||
+ | \begin{array}{ll} | ||
+ | \mathbf{X}' | ||
+ | \mathbf{Z}' | ||
+ | \end{array} | ||
+ | \right] | ||
+ | \left[ | ||
+ | \begin{array}{c} | ||
+ | \mathbf{\hat{b}}\\ | ||
+ | \mathbf{\hat{u}} | ||
+ | \end{array} | ||
+ | \right] | ||
+ | = | ||
+ | \left[ | ||
+ | \begin{array}{c} | ||
+ | \mathbf{X}' | ||
+ | \mathbf{Z}' | ||
+ | \end{array} | ||
+ | \right] | ||
+ | \) | ||
- | Set block size for preconditioner (default 1). | + | where $\mathbf{H}$ is a matrix combining additive genetic relationship matrices and a genomic relationship matrix. |
- | OPTION SNP_file snp | + | \( |
+ | \mathbf{H}^{-1} | ||
+ | = | ||
+ | \mathbf{A}^{-1} | ||
+ | + | ||
+ | \left[ | ||
+ | \begin{array}{cc} | ||
+ | \mathbf{0} & \mathbf{0} \\ | ||
+ | \mathbf{0} & \tau\mathbf{G}^{-1}-\omega\mathbf{A}_{22}^{-1} | ||
+ | \end{array} | ||
+ | \right] | ||
+ | \) | ||
- | Specify | + | 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. | ||
readme.blupf90.txt · Last modified: 2024/05/15 19:00 by dani