readme.renumf90
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| readme.renumf90 [2020/04/21 07:10] – yutaka | readme.renumf90 [2024/03/25 18:22] (current) – external edit 127.0.0.1 | ||
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| * missing animals have code 0; 00 may be treated as a known animal | * missing animals have code 0; 00 may be treated as a known animal | ||
| + | \\ | ||
| + | **Hint**: type '' | ||
| =====Structure of parameter file====== | =====Structure of parameter file====== | ||
| Line 37: | Line 38: | ||
| =====Fields in the parameter file===== | =====Fields in the parameter file===== | ||
| - | # Parameter file for program renf90; it is translated | + | # Parameter file for renumf90. It is translated |
| - | # file for BLUPF90 family of programs. | + | |
| Lines with # are treated as comments | Lines with # are treated as comments | ||
| Line 68: | Line 68: | ||
| < | < | ||
| WEIGHT(S) | WEIGHT(S) | ||
| - | w | + | w1 [w2 w3...wn] |
| </ | </ | ||
| - | w is | + | w1 [w2 w3...wn] are |
| < | < | ||
| Line 86: | Line 86: | ||
| positions can be different for each trait for fixed effects; | positions can be different for each trait for fixed effects; | ||
| - | for random effects, only one position + 0 (misising) efefct are | + | for random effects, only one position + 0 (missing) efefct are |
| possible. | possible. | ||
| * type is ' | * type is ' | ||
| - | * form is ' | + | * for crossclassified effects: |
| + | * for covariables: | ||
| < | < | ||
| Line 183: | Line 184: | ||
| the default is 3 | the default is 3 | ||
| - | all pedigrees are loaded if p=0. | + | all pedigrees are loaded if p=0. This is the fastest as it reads the pedigree file only once. However, if you want to extract the informative animals (genotyped and phenotyped animals + their ancestors traced back) put a large number like 100. With p=0, RENUMF90 tries to include all animals found in the raw pedigree file even if the animals in the pedigree are not related to the animals with phenotype or genotype. Thus, p=0 is not recommended unless your pedigree file is already prepared and consists in the informative animals or the animals of interest. |
| < | < | ||
| Line 226: | Line 228: | ||
| </ | </ | ||
| optional\\ | optional\\ | ||
| - | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file | + | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file. Inbreeding calculation is a default in RENUMF90 ≥ v1.157, even if this keyword is not used. |
| // | // | ||
| * ' | * ' | ||
| - | * ' | + | * ' |
| + | * 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation | ||
| + | * ' | ||
| < | < | ||
| Line 249: | Line 253: | ||
| //r_type// could be: | //r_type// could be: | ||
| * ' | * ' | ||
| - | * " | + | * " |
| < | < | ||
| Line 258: | Line 262: | ||
| * //r1-rq// specifies positions of covariables if r_type=' | * //r1-rq// specifies positions of covariables if r_type=' | ||
| - | * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type=' | + | * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type=' |
| < | < | ||
| Line 337: | Line 341: | ||
| where //nn// is the new size. | where //nn// is the new size. | ||
| - | - the maximun | + | - the maximum |
| < | < | ||
| OPTION max_field_readline nn | OPTION max_field_readline nn | ||
| Line 343: | Line 347: | ||
| where //nn// is the number of fields. | where //nn// is the number of fields. | ||
| + | < | ||
| + | OPTION missing x | ||
| + | </ | ||
| + | |||
| + | allows indicating that missing value is the number x (e.g. 999) for instance if 0 is a valid record. | ||
| + | |||
| + | < | ||
| + | OPTION missing_in_weights | ||
| + | </ | ||
| + | |||
| + | in addition, this indicates that if a weight for the trait is 0, then the value of the trait is converted to " | ||
| + | |||
| + | < | ||
| + | OPTION no_basic_statistics | ||
| + | </ | ||
| + | avoids the computation of basic statistics (min, max, correlations...) which take a certain time for very large data file. | ||
| + | |||
| + | < | ||
| + | OPTION inbreeding_method 1 | ||
| + | </ | ||
| + | |||
| + | allows choosing a method for inbreeding calculation. The inbreeding coefficients are used later (in the other programs) to set up the coefficients for the A-inverse. Existing options are: | ||
| + | |||
| + | * 7: Recursive tabular with self breeding generations . This method is for populations with selfing, i.e. wheat. | ||
| + | * 6: Hybrid parallel computing which is basically a parallel (OMP) version of Meuwissen and Luo (1992) | ||
| + | * 5: method of Tier (1990) | ||
| + | * 4: recursive tabular method | ||
| + | * 3: Modified Colleau by Sargolzaei et al. (2005) | ||
| + | * 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004) | ||
| + | * 1: Meuwissen and Luo (1992) | ||
| + | |||
| + | the default is method 1. Large speed-ups are made using method 6 but this requires using several threads (e.g. using '' | ||
| The end of the parameter file for '' | The end of the parameter file for '' | ||
| Line 380: | Line 416: | ||
| 2) parent 1 number or unknown parent group number for parent 1 | 2) parent 1 number or unknown parent group number for parent 1 | ||
| 3) parent 2 number or unknown parent group number for parent 2 | 3) parent 2 number or unknown parent group number for parent 2 | ||
| - | 4) 3 minus number of known parents | + | 4) 3 minus number of known parents |
| 5) known or estimated year of birth (0 if not provided) | 5) known or estimated year of birth (0 if not provided) | ||
| 6) number of known parents (parents might be eliminated if not contributing; | 6) number of known parents (parents might be eliminated if not contributing; | ||
readme.renumf90.1587453036.txt.gz · Last modified: 2024/03/25 18:22 (external edit)