readme.renumf90
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readme.renumf90 [2018/05/30 17:51] – 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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* if t is ' | * if t is ' | ||
+ | |||
+ | * There are the other values for t: ' | ||
+ | |||
< | < | ||
INBREEDING | INBREEDING | ||
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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 | ||
+ | * ' | ||
< | < | ||
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==== User-defined UPG code ==== | ==== User-defined UPG code ==== | ||
- | The program accepts the following keywords in '' | + | See [[undoc: |
- | | + | The program accepts one of the following keywords in '' |
- | group | + | With one of these options, the program looks at a particular column in the pedigree file as a group code and use it for assigning the UPG code. If an animal has a missing parent, the program assigns a UPG code based on the group code. |
- | + | ||
- | or | + | |
- | + | ||
- | UPG_TYPE | + | |
- | group_unisex | + | |
- | With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns | + | * '' |
+ | * '' | ||
+ | * '' | ||
- | The column in the pedigree file is specified with the 6th item in '' | + | For '' |
FILE_POS | FILE_POS | ||
1 2 3 0 0 5 | 1 2 3 0 0 5 | ||
- | The program now accept 3 items, 5 items, or 6 items in '' | + | For '' |
+ | FILE_POS | ||
+ | 1 2 3 0 0 5 6 | ||
+ | The program now accept 3, 5, 6, or 7 items in '' | ||
=====Extra comments===== | =====Extra comments===== | ||
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parameters used to read the input file: | parameters used to read the input file: | ||
- | - the default size of character fields | + | - the default size of character fields |
< | < | ||
OPTION alpha_size nn | OPTION alpha_size nn | ||
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where //nn// is the new size. | where //nn// is the new size. | ||
- | - the size of th record length | + | - the size of th record length |
< | < | ||
OPTION max_string_readline nn | OPTION max_string_readline nn | ||
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where //nn// is the new size. | where //nn// is the new size. | ||
- | - the maximun number of fields | + | - the maximun number of fields |
< | < | ||
OPTION max_field_readline nn | OPTION max_field_readline nn |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani