readme.thrgibbs1
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| readme.thrgibbs1 [2013/07/17 16:23] – shogo | readme.thrgibbs1 [2016/10/17 19:52] – [Options] shogo | ||
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| =====Summary===== | =====Summary===== | ||
| - | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90. Rewritten by Shogo Tsuruta in 2004. See PREGSF90 with genotypes (SNP) for options. | + | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90 |
| \\ | \\ | ||
| THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated or assumed. Another version of thrgibbs1f90b for binary responses is available. | THRGIBBS1F90 implements Gibbs sampler for mixed threshold-linear models involving multiple categorical and linear variables. Thresholds and variances can be estimated or assumed. Another version of thrgibbs1f90b for binary responses is available. | ||
| + | \\ | ||
| + | See PREGSF90 with genotypes (SNP) for options. | ||
| =====Parameters===== | =====Parameters===== | ||
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| OPTION fixed_var all 1 2 3 | OPTION fixed_var all 1 2 3 | ||
| </ | </ | ||
| - | Store all samples for solutions in " | + | Store all samples for solutions in " |
| < | < | ||
| OPTION fixed_var mean | OPTION fixed_var mean | ||
| </ | </ | ||
| - | Only posterior means and SD for solutions are calculated for all effects in " | + | Only posterior means and SD for solutions are calculated for all effects in " |
| < | < | ||
| OPTION fixed_var mean 1 2 3 | OPTION fixed_var mean 1 2 3 | ||
| - | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | + | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " |
| </ | </ | ||
| < | < | ||
| OPTION solution all | OPTION solution all | ||
| </ | </ | ||
| - | Store all samples for solutions in " | + | Store all samples for solutions in " |
| < | < | ||
| OPTION solution all 1 2 3 | OPTION solution all 1 2 3 | ||
| </ | </ | ||
| - | Store all samples for solutions in " | + | Store all samples for solutions in " |
| < | < | ||
| OPTION solution mean | OPTION solution mean | ||
| </ | </ | ||
| - | Only posterior means and SD for solutions are calculated for all effects in " | + | Only posterior means and SD for solutions are calculated for all effects in " |
| < | < | ||
| OPTION solution mean 1 2 3 | OPTION solution mean 1 2 3 | ||
| </ | </ | ||
| - | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | + | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " |
| < | < | ||
| OPTION cont 10000 | OPTION cont 10000 | ||
| </ | </ | ||
| - | " | + | " |
| < | < | ||
| OPTION prior 5 2 -1 5 | OPTION prior 5 2 -1 5 | ||
| Line 68: | Line 70: | ||
| Set the fixed thresholds. No need to set 0 for binary traits. | Set the fixed thresholds. No need to set 0 for binary traits. | ||
| < | < | ||
| - | OPTION residual 1. | + | OPTION residual 1 |
| </ | </ | ||
| Set the residual variance = 1. | Set the residual variance = 1. | ||
| < | < | ||
| - | OPTION | + | OPTION |
| </ | </ | ||
| - | Negative values | + | Specify checking pos-def for fixed effects. |
| + | < | ||
| + | OPTION censored 1 0 | ||
| + | </ | ||
| + | Negative values | ||
| + | < | ||
| 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. | ||
| - | |||
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1