readme.thrgibbs1
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readme.thrgibbs1 [2012/05/29 13:11] – shogo | readme.thrgibbs1 [2016/10/17 19:52] – [Options] shogo | ||
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- | =====THRGIBBS1F90===== | + | ====== THRGIBBS1F90 ====== |
- | // | + | |
- | + | ||
- | Gibbs sampler for threshold-linear mixed models | + | |
=====Summary===== | =====Summary===== | ||
- | Based on THRGIBBSF90 written by DeukHwan Lee at the University of Georgia, | + | 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 | |
- | =====Functionality===== | + | \\ |
- | THRGIBBS1F90 | + | See PREGSF90 with genotypes (SNP) for options. |
- | involving multiple categorical and linear variables. Thresholds and variances | + | |
- | can be computed | + | |
=====Parameters===== | =====Parameters===== | ||
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OPTION cat 0 0 2 5 | OPTION cat 0 0 2 5 | ||
</ | </ | ||
- | 0s indicate that the first and second traits are linear. | + | " |
- | 2 and 5 indicate that the third and fourth traits are categorical with 2 and 5 categories. | + | "2" |
< | < | ||
OPTION fixed_var all | OPTION fixed_var all | ||
</ | </ | ||
- | Store all samples for solutions in " | + | Store all samples for solutions in " |
- | assuming that (co)variances | + | |
< | < | ||
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 | ||
</ | </ | ||
- | 10000 is the number of samples run previously. | + | "10000" |
- | The user can restart the program from the last run. | + | |
< | < | ||
- | OPTION prior 10 | + | OPTION prior 5 2 -1 5 |
</ | </ | ||
- | 10 is the degree of belief for the priors specified in the parameter file. | + | 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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OPTION thresholds 0.0 1.0 2.0 | OPTION thresholds 0.0 1.0 2.0 | ||
</ | </ | ||
- | Set the fixed the thresholds | + | Set the fixed thresholds. No need to set 0 for binary traits. |
- | 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 of the last category in the data set indicate censored records. " | + | Specify checking pos-def for fixed effects. |
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
- | Change the missing value for a continuous | + | 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