readme.thrgibbs1
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readme.thrgibbs1 [2013/09/30 17:04] – 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 |
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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. | ||
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OPTION fixed_var all 1 2 3 | OPTION fixed_var all 1 2 3 | ||
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- | Store all samples for solutions in " | + | Store all samples for solutions in " |
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OPTION fixed_var mean | OPTION fixed_var mean | ||
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- | 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 " |
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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 " |
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OPTION solution mean | OPTION solution mean | ||
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- | 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 " |
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OPTION solution mean 1 2 3 | OPTION solution mean 1 2 3 | ||
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- | 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 | ||
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- | " | + | " |
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OPTION prior 5 2 -1 5 | OPTION prior 5 2 -1 5 | ||
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Set the fixed thresholds. No need to set 0 for binary traits. | Set the fixed thresholds. No need to set 0 for binary traits. | ||
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- | OPTION residual 1. | + | OPTION residual 1 |
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Set the residual variance = 1. | Set the residual variance = 1. | ||
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- | OPTION | + | OPTION |
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- | Negative values | + | Specify checking pos-def for fixed effects. |
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+ | OPTION censored 1 0 | ||
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+ | Negative values | ||
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OPTION SNP_file snp | OPTION SNP_file snp | ||
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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