readme.blupf90
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readme.blupf90 [2012/05/30 00:55] – [BLUPF90] ignacio | readme.blupf90 [2024/05/15 18:58] – dani | ||
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====== BLUPF90 ====== | ====== BLUPF90 ====== | ||
- | The documentation for blupf90 is available separately as a {{: | + | ===== Summary ===== |
+ | The documentation for blupf90 is available separately as a {{: | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
< | < | ||
OPTION conv_crit 1e-12 | OPTION conv_crit 1e-12 | ||
</ | </ | ||
- | Set convergence criteria (deault | + | Set convergence criteria (default |
< | < | ||
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 | ||
Line 22: | Line 26: | ||
OPTION sol se | OPTION sol se | ||
</ | </ | ||
- | Store solutions and s.e. | + | 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 | OPTION missing -999 | ||
</ | </ | ||
- | Missing observation | + | Specify missing observations in the data file. Must be an integer value (default |
< | < | ||
OPTION residual | OPTION residual | ||
</ | </ | ||
- | y-hat and residual will be shown in yhat_residual. | + | y-hat and residual will be included |
< | < | ||
OPTION blksize 3 | OPTION blksize 3 | ||
</ | </ | ||
- | Set block size for preconditioner (default 1). | + | Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multi-trait model, use the number of traits. This option is extremely important to ensure convergence in multi-trait models. |
+ | < | ||
+ | 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 | OPTION SNP_file snp | ||
</ | </ | ||
Specify the SNP file name to use genotype data. | Specify the SNP file name to use genotype data. | ||
+ | |||
+ | < | ||
+ | OPTION snp_p_value | ||
+ | </ | ||
+ | Computes the elements of the inverse of the Mixed Model Equations that are needed for exact GWAS with p-values using postGSf90. This requires quite a lot of memory and time. For details see https:// | ||
+ | |||
+ | ==== 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. | ||
+ |
readme.blupf90.txt · Last modified: 2024/05/15 19:00 by dani