readme.renumf90
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| readme.renumf90 [2018/06/05 23:50] – [Options] dani | readme.renumf90 [2024/05/22 18:53] (current) – [Options] dani | ||
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| =======RENUMF90====== | =======RENUMF90====== | ||
| A renumbering program for the '' | A renumbering program for the '' | ||
| Line 21: | Line 20: | ||
| * 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 37: | ||
| =====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 67: | ||
| < | < | ||
| WEIGHT(S) | WEIGHT(S) | ||
| - | w | + | w1 [w2 w3...wn] |
| </ | </ | ||
| - | w is | + | w1 [w2 w3...wn] are |
| < | < | ||
| Line 86: | Line 85: | ||
| 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 183: | ||
| 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 218: | Line 219: | ||
| * if t is ' | * if t is ' | ||
| + | |||
| + | * There are the other values for t: ' | ||
| + | |||
| < | < | ||
| INBREEDING | INBREEDING | ||
| Line 223: | Line 227: | ||
| </ | </ | ||
| 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 246: | Line 252: | ||
| //r_type// could be: | //r_type// could be: | ||
| * ' | * ' | ||
| - | * " | + | * " |
| < | < | ||
| Line 255: | Line 261: | ||
| * //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 281: | Line 287: | ||
| ==== 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===== | ||
| Line 319: | Line 325: | ||
| =====Options===== | =====Options===== | ||
| - | The following options can added at the end of the parameter file to redefine | + | The following options can be added at the end of the parameter file to redefine |
| parameters used to read the input file: | parameters used to read the input file: | ||
| Line 328: | Line 334: | ||
| where //nn// is the new size. | where //nn// is the new size. | ||
| - | - the size of th record length (default = 800) | + | - the size of the record length (default = 800) |
| < | < | ||
| OPTION max_string_readline nn | OPTION max_string_readline nn | ||
| Line 334: | Line 340: | ||
| 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 340: | Line 346: | ||
| 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 remove_all_missing | ||
| + | </ | ||
| + | |||
| + | removes lines in the data where phenotypes are missing. Keeping those lines may cause unexpected behavior in some programs. | ||
| + | |||
| + | < | ||
| + | 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, | ||
| + | |||
| + | < | ||
| + | OPTION inbreeding_method m | ||
| + | </ | ||
| + | |||
| + | 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. Acceptable values for m are: | ||
| + | | ||
| + | 1: Meuwissen and Luo (1992) | ||
| + | 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004) | ||
| + | 3: Modified Colleau by Sargolzaei et al. (2005) | ||
| + | 4: recursive tabular method | ||
| + | 5: method of Tier (1990) | ||
| + | 6: Hybrid parallel computing, which is basically a parallel (OMP) version of Meuwissen and Luo (1992) | ||
| + | 7: Recursive tabular with self-breeding generations. For populations with selfing, i.e., wheat | ||
| + | |||
| + | 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 '' | ||
| - | All of these lines are passed to parameter file renf90.par to be used by application programs. | + | All of these lines are passed to the parameter file renf90.par to be used by application programs. |
| Line 377: | Line 421: | ||
| 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.txt · Last modified: 2024/05/22 18:53 by dani