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--- readme.blupf90 [2012/05/28 14:34] – shogo
+++ readme.blupf90 [2024/03/25 18:22] – external edit 127.0.0.1
@@ Line 1: / Line 1: @@
-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 =====
+<file>
 OPTION conv_crit 1e-12
+</file>
-    Set convergence criteria (deault 1e-12).
+Set convergence criteria (deault 1e-12).
+<file>
 OPTION maxrounds 10000
+</file>
-    Set maximum number of rounds (default 1000).
+Set maximum number of rounds (default 5000).
+<file>
 OPTION solv_method FSPAK
+</file>
-    Selection solutions by FSPAK, SOR or PCG (default PCG).
+Selection solutions by FSPAK, SOR or PCG (default PCG).
+<file>
 OPTION r_factor 1.6
+</file>
+Set relaxation factor for SOR (default 1.4).
+<file>
+OPTION sol se
+</file>
+Store solutions and standard errors.
+<file>
+OPTION store_pev_pec 6
+</file>
+Store triangular matrices of standard errors and its covariances for correlated random effects such as direct-maternal effects and random-regression effects in "pev_pec_bf90".
+<file>
+OPTION missing -999
+</file>
+Specify missing observations (default 0) in integer.
+<file>
+OPTION residual
+</file>
+y-hat and residual will be included in "yhat_residual".
+<file>
+OPTION blksize 3
+</file>
+Set a block size for preconditioner (default 1) to accelerate convergence (usually 2 to 5 times faster). For a multiple-trait model, use the number of traits.
+<file>
+OPTION prior_solutions
+</file>
+Using the previous solution file to start the iteration. An additional software is required to use this option.
+<file>
+OPTION stdresidual
+</file>
+y-hat and student residuals will be included in "yhat_student_residual".
+<file>
+OPTION check_levels 0
+</file>
+Check levels (default 1 = true).
+<file>
+OPTION use_yams
+</file>
+Run the program with YAMS (modified FSPAK).
+<file>
+OPTION SNP_file snp
+</file>
+Specify the SNP file name to use genotype data.
-    Set relaxation factor for SOR (default 1.4).
+<file>
+OPTION snp_p_value
+</file>
+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://doi.org/10.1101/555243.
-OPTION sol se
+==== Omit A-inverse ====
-    Store solutions and s.e.
+    OPTION omit_ainv
-OPTION missing -999
+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.
-    Missing observation (default 0).
+    OPTION omit_ainv
+    OPTION TauOmega 1.0 0.0
+    OPTION AlphaBeta 0.95 0.05
-OPTION residual
+With the above options, the program doesn't create $\mathbf{A}^{-1}$ but calculates $\tau\mathbf{G}^{-1}-\omega\mathbf{A}_{22}^{-1}$. When the omega ($\omega$) is zero, only $\mathbf{G}^{-1}$ will be included in the equations. $\mathbf{G}$ is blended with $\mathbf{A}_{22}$ as $\alpha\mathbf{G}+\beta\mathbf{A}_{22}$ before the inversion ($\alpha=0.95$ and $\beta=0.05$ in this case).
-    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
+\(
+\left[
+\begin{array}{ll}
+\mathbf{X}'\mathbf{X} & \mathbf{X}'\mathbf{Z}\\
+\mathbf{Z}'\mathbf{X} & \mathbf{Z}'\mathbf{Z} + \lambda\mathbf{H}^{-1}
+\end{array}
+\right]
+\left[
+\begin{array}{c}
+\mathbf{\hat{b}}\\
+\mathbf{\hat{u}}
+\end{array}
+\right]
+=
+\left[
+\begin{array}{c}
+\mathbf{X}'\mathbf{y}\\
+\mathbf{Z}'\mathbf{y}
+\end{array}
+\right]
+\)
-    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 the SNP file name to use genotype data.
+If we omit $\mathbf{A}^{-1}$ and $\mathbf{A}_{22}^{-1}$, the equations are equivalent to GBLUP.
+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.