readme.thrgibbs1
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readme.thrgibbs1 [2012/05/29 13:19] – shogo | readme.thrgibbs1 [2014/05/08 10:58] – shogo | ||
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====== THRGIBBS1F90 ====== | ====== THRGIBBS1F90 ====== | ||
- | \\ | ||
- | Gibbs sampler for threshold-linear mixed models | ||
=====Summary===== | =====Summary===== | ||
- | + | Gibbs sampler for threshold-linear mixed models. The original program (THRGIBBSF90) was written by DeukHwan Lee in 2001 based on GIBBS2F90 | |
- | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, | + | \\ |
- | + | ||
- | + | ||
- | =====Functionality===== | + | |
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 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 | ||
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OPTION cont 10000 | OPTION cont 10000 | ||
</ | </ | ||
- | " | + | " |
- | The user can restart the program from the last run. | + | |
< | < | ||
- | 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 | ||
Line 68: | Line 68: | ||
OPTION thresholds 0.0 1.0 2.0 | OPTION thresholds 0.0 1.0 2.0 | ||
</ | </ | ||
- | 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 censored xx | + | OPTION censored xx. |
</ | </ | ||
Negative values of the last category in the data set indicate censored records. " | Negative values of the last category in the data set indicate censored records. " | ||
- | + | < | |
+ | 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