readme.thrgibbs1
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readme.thrgibbs1 [2012/05/29 17:07] – shogo | readme.thrgibbs1 [2017/10/26 08:45] – [Options] shogo | ||
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====== THRGIBBS1F90 ====== | ====== THRGIBBS1F90 ====== | ||
- | \\ | ||
- | 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. | ||
=====Summary===== | =====Summary===== | ||
+ | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90 and formulas by Rob Tempelman. Rewritten by Shogo Tsuruta in 2004. See PREGSF90 with genotypes (SNP) for options. | ||
+ | \\ | ||
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 | ||
</ | </ | ||
- | " | + | " |
+ | When using " | ||
< | < | ||
- | OPTION prior 5 | + | OPTION prior 5 2 -1 5 |
</ | </ | ||
- | " | + | The (co)variance |
+ | Degree of belief for all random effects should be specified using the following structure: | ||
+ | OPTION prior eff1 db1 eff2 db2 ... effn dbn -1 dbres\\ | ||
+ | effx correspond to the effect number and dbx to the degree of belief for this random effect, -1 corresponds to the degree of belief of the residual variance.\\ | ||
+ | In this example 2 is the degree of belief for the 5th effect, and 5 is the degree of belief for the residual.\\ | ||
< | < | ||
OPTION seed 123 -432 | OPTION seed 123 -432 | ||
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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. | ||
< | < | ||
- | OPTION residual 1. | + | OPTION residual 1 |
</ | </ | ||
- | Set the residual variance = 1. | + | Set the residual variance = 1 (no need for binary traits). |
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | Negative values | + | Specify checking pos-def for fixed effects where x.x is a tolerance (default=1d-08). |
- | + | < | |
+ | OPTION censored 1 0 | ||
+ | </ | ||
+ | Negative values | ||
+ | < | ||
+ | OPTION SNP_file snp | ||
+ | </ | ||
+ | Specify the SNP file name to use genotype data. |
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1