readme.renumf90
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readme.renumf90 [2016/10/13 21:58] – [Fields in the parameter file] ignacio | readme.renumf90 [2024/05/15 18:32] – [Options] dani | ||
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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 | ||
Line 47: | Line 47: | ||
</ | </ | ||
The data file is f1 | The data file is f1 | ||
+ | |||
+ | < | ||
+ | SKIP_HEADER | ||
+ | n | ||
+ | </ | ||
+ | This is optional. It skips the first n lines as header in the data file. | ||
< | < | ||
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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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// | // | ||
+ | |||
+ | < | ||
+ | SKIP_HEADER | ||
+ | n | ||
+ | </ | ||
+ | This is optional. It skips the first n lines as header in the pedigree file. | ||
< | < | ||
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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. |
- | * if inb_type is ' | + | |
- | * if inb_type is ' | + | // |
+ | * ' | ||
+ | * ' | ||
+ | * 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation | ||
+ | * ' | ||
+ | |||
+ | < | ||
+ | FIXED_REGRESSION | ||
+ | r_type | ||
+ | </ | ||
+ | It is the same as '' | ||
< | < | ||
RANDOM_REGRESSION | RANDOM_REGRESSION | ||
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//r_type// could be: | //r_type// could be: | ||
* ' | * ' | ||
- | * " | + | * " |
< | < | ||
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* //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=' |
< | < | ||
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</ | </ | ||
//gmpe// are (co)variances for the MPE effect if present | //gmpe// are (co)variances for the MPE effect if present | ||
+ | |||
+ | |||
+ | ==== User-defined UPG code ==== | ||
+ | |||
+ | See [[undoc: | ||
+ | |||
+ | The program accepts one of the following keywords in '' | ||
+ | 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. | ||
+ | |||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | |||
+ | For '' | ||
+ | |||
+ | FILE_POS | ||
+ | 1 2 3 0 0 5 | ||
+ | |||
+ | 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 | + | - the maximum |
< | < | ||
OPTION max_field_readline nn | OPTION max_field_readline nn | ||
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where //nn// is the number of fields. | where //nn// is the number of fields. | ||
+ | < | ||
+ | OPTION missing x | ||
+ | </ | ||
+ | |||
+ | allows indicating that the missing value is the number x (e.g., 999), for instance, if 0 is a valid record. This is only to represent the missing value in the data. If there are covariables in the data, 0 is treated as a value, not missing information. Missing pedigree is always 0 and cannot be changed to another value. | ||
+ | |||
+ | < | ||
+ | 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 '' | ||
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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; | ||
if animal has genotype 10+number of know parents | if animal has genotype 10+number of know parents | ||
7) number of records | 7) number of records | ||
- | 8) number of progenies | + | 8) number of progeny |
- | 9) number of progenies | + | 9) number of progeny |
10) original animal id | 10) original animal id | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani