readme.renumf90
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readme.renumf90 [2012/05/29 12:35] – [Fields in the parameter file] ignacio | readme.renumf90 [2023/01/25 12:46] – [Fields in the parameter file] andres | ||
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=======RENUMF90====== | =======RENUMF90====== | ||
- | renumbering program for the BLUPF90 family now works with SNP info\\ | + | A renumbering program for the '' |
Ignacy Misztal and Ignacio Aguilar, University of Georgia\\ | Ignacy Misztal and Ignacio Aguilar, University of Georgia\\ | ||
August 27, 2001 - Mar 17, 2011 | August 27, 2001 - Mar 17, 2011 | ||
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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 | ||
| | ||
- | < | + | < |
DATAFILE | DATAFILE | ||
f1 | f1 | ||
Line 48: | Line 48: | ||
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. | ||
+ | |||
+ | < | ||
TRAITS | TRAITS | ||
t1 t2 .. tn | t1 t2 .. tn | ||
Line 62: | Line 68: | ||
< | < | ||
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: | ||
< | < | ||
Line 101: | Line 108: | ||
rtype is: | rtype is: | ||
* ' | * ' | ||
- | * ' | + | * ' |
* ' | * ' | ||
Line 113: | Line 120: | ||
* ' | * ' | ||
* ' | * ' | ||
- | * ' | + | * ' |
< | < | ||
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// | // | ||
+ | |||
+ | < | ||
+ | SKIP_HEADER | ||
+ | n | ||
+ | </ | ||
+ | This is optional. It skips the first n lines as header in the pedigree file. | ||
< | < | ||
Line 131: | Line 144: | ||
for animal effect only; | for animal effect only; | ||
- | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam | + | specifies positions in the pedigree file of animal |
missing alt_dam or yob can be replaced by 0 | missing alt_dam or yob can be replaced by 0 | ||
Line 170: | Line 184: | ||
the default is 3 | the default is 3 | ||
- | all pedigrees are loaded if p=0. | + | all pedigrees are loaded if p=0. To consider all ancestors to be traced back from genotyped and phenotyped animals, 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. |
< | < | ||
Line 204: | Line 219: | ||
* if t is ' | * if t is ' | ||
- | * if t is ' | + | * if t is ' |
+ | |||
+ | * There are the other values for t: ' | ||
+ | |||
+ | < | ||
+ | INBREEDING | ||
+ | inb_type | ||
+ | </ | ||
+ | optional\\ | ||
+ | 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 | ||
+ | * ' | ||
+ | |||
+ | < | ||
+ | FIXED_REGRESSION | ||
+ | r_type | ||
+ | </ | ||
+ | It is the same as '' | ||
< | < | ||
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</ | </ | ||
Specifies that random regressions should be applied to the animal and | Specifies that random regressions should be applied to the animal and | ||
- | corresponding effects (mat, pe and mpe) | + | corresponding |
this keyword also could be applied to set covariables for fixed effects; | this keyword also could be applied to set covariables for fixed effects; | ||
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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 | + | OPTION |
</ | </ | ||
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 |
</ | </ | ||
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 |
</ | </ | ||
where //nn// is the number of fields. | where //nn// is the number of fields. | ||
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</ | </ | ||
catenates //b c// ... into //a//.\\ | catenates //b c// ... into //a//.\\ | ||
- | Keywords | + | Keyword |
There may be many combined fields. | There may be many combined fields. | ||
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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 | + | 6) number of known parents (parents might be eliminated if not contributing; |
- | | + | |
7) number of records | 7) number of records | ||
- | 8) number of progenies | + | 8) number of progeny |
- | | + | 9) number of progeny |
- | 9) number of progenies | + | |
- | | + | |
10) original animal id | 10) original animal id | ||
Line 372: | Line 429: | ||
< | < | ||
# Parameter file for program renf90; it is translated to parameter | # Parameter file for program renf90; it is translated to parameter | ||
- | # file for BLUPF90 family | + | # file for BLUPF90 family programs. |
DATAFILE | DATAFILE | ||
data.test | data.test |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani