readme.reml
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.reml [2012/05/29 14:30] – shogo | readme.reml [2014/11/25 11:34] – shogo | ||
---|---|---|---|
Line 2: | Line 2: | ||
===== Summary ===== | ===== Summary ===== | ||
+ | The variance component estimation program with EM-REML algorithm. The final results will be saved in " | ||
+ | \\ | ||
+ | See PREGSF90 with genotypes (SNP) for options. | ||
===== Options ===== | ===== Options ===== | ||
Line 7: | Line 10: | ||
OPTION conv_crit1d-12 | OPTION conv_crit1d-12 | ||
</ | </ | ||
- | | + | Convergence criterion (default 1d-10). |
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | | + | Maximum rounds (default 5000). |
+ | < | ||
+ | OPTION sol se | ||
+ | </ | ||
+ | Store solutions and se. | ||
+ | < | ||
+ | OPTION residual | ||
+ | </ | ||
+ | y-hat and residuals will be included in " | ||
+ | < | ||
+ | OPTION missing -999 | ||
+ | </ | ||
+ | Specify missing observations (default 0). | ||
+ | < | ||
+ | OPTION use_yams | ||
+ | </ | ||
+ | Run the program with YAMS (modified FSPAK). The computing time can be dramatically improved. | ||
< | < | ||
OPTION constant_var 5 1 2 | OPTION constant_var 5 1 2 | ||
</ | </ | ||
- | The effect number | + | 5: effect number\\ |
+ | 1: first trait number\\ | ||
+ | 2: second trait number\\ | ||
+ | implying the covariance between traits 1 and 2 for effect 5. | ||
< | < | ||
OPTION SNP_file snp | OPTION SNP_file snp | ||
</ | </ | ||
- | | + | Specify the SNP file name to use genotype data. |
- | ===== Does remlf90 | + | ===== Does REMLF90 |
- | < | + | When the expected variance is very small or the covariance matrix is close to non-positive definite, try with two different starting values (e.g., much smaller = 0.00001 and much bigger = 1000 when the expected variance |
- | Even when there is no variance, remlf90 | + | |
- | </ | + | The REMLF90 program |
+ | If AIREMLF90 does not converge but REMLF90 converges with the same data set and the same model, rerun REMLF90 with a small starting value to check the estimate because it could be artifact. |
readme.reml.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1