readme.renumf90
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readme.renumf90 [2020/04/21 07:10] – yutaka | readme.renumf90 [2023/03/02 00:47] – andres | ||
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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====== | ||
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=====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 | ||
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< | < | ||
WEIGHT(S) | WEIGHT(S) | ||
- | w | + | w1 [w2 w3...wn] |
</ | </ | ||
- | w is | + | w1 [w2 w3...wn] are |
< | < | ||
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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: | ||
< | < | ||
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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. |
< | < | ||
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</ | </ | ||
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 | ||
+ | * ' | ||
< | < |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani