readme.renumf90
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readme.renumf90 [2012/05/29 12:28] – [Options] ignacio | readme.renumf90 [2012/05/29 12:38] – [RENUMF90] ignacio | ||
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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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e1.. en type form | e1.. en type form | ||
</ | </ | ||
- | this line defines one group of effects; e1 .. en are positions of this effect for all traits;\\ | + | this line defines one group of effects; e1 .. en are positions of this effect for all traits; |
- | 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 (misising) efefct are | ||
possible. | possible. | ||
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d1 .. dn form | d1 .. dn form | ||
</ | </ | ||
- | optional for covariables only, specifies nesting;\\ | + | optional for covariables only, specifies nesting; |
form is as above | form is as above | ||
| | ||
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the RANDOM keyword occurs only if the current effect is random; | the RANDOM keyword occurs only if the current effect is random; | ||
- | rtype is ' | + | rtype is: |
+ | * ' | ||
+ | * ' | ||
+ | * ' | ||
< | < | ||
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o1 o2.. oq | o1 o2.. oq | ||
</ | </ | ||
- | causes extra effects appended to the animal effect;\\ | + | causes extra effects appended to the animal effect; |
- | current options include | + | |
+ | current options include: | ||
* ' | * ' | ||
* ' | * ' | ||
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</ | </ | ||
- | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only |
+ | |||
+ | //fped// specifies the pedigree file | ||
< | < | ||
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</ | </ | ||
- | for animal effect only;\\ | + | for animal effect only; |
specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ | ||
- | missing alt_dam or yob can be replaced by 0\\ | + | missing alt_dam or yob can be replaced by 0 |
- | if this line is not given, defaults are 1 2 3 0 0.\\ | + | |
- | If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam;\\ If alt_dam field is not zero, it should include ID of real or recipient dam. | + | if this line is not given, defaults are 1 2 3 0 0. |
+ | |||
+ | If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam; | ||
+ | |||
+ | If alt_dam field is not zero, it should include ID of real or recipient dam. | ||
< | < | ||
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optional;\\ | optional;\\ | ||
- | //fsnp// specifies files with ID and SNP information; | + | //fsnp// specifies files with ID and SNP information; |
if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will | if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will | ||
- | include the genomic information; | + | include the genomic information; |
- | file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and | + | |
- | include digits 0, 1, 2 and 5;\\ | + | file //fsnp// should start with ID with the same format as fped and SNP info needs to start from a fixed column and |
+ | include digits 0, 1, 2 and 5; | ||
+ | |||
ID and SNP info need to be separated by at leats one space; see info for program [[readme.pregsf90|PreGSf90]] | ID and SNP info need to be separated by at leats one space; see info for program [[readme.pregsf90|PreGSf90]] | ||
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</ | </ | ||
- | optional\\ | + | optional |
- | for animal effect only;\\ | + | |
- | p specifies the depth of pedigree search;\\ | + | for animal effect only; |
- | the default is 3; all pedigrees are loaded if p=0. | + | |
+ | //p// specifies the depth of pedigree search; | ||
+ | |||
+ | the default is 3 | ||
+ | |||
+ | all pedigrees are loaded if p=0. | ||
< | < | ||
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min avg max | min avg max | ||
</ | </ | ||
- | optional\\ | + | optional |
- | specifies minimum, average and maximum generation interval;\\ | + | |
+ | specifies minimum, average and maximum generation interval | ||
applicable only if year of birth present; minimum and maximum used for | applicable only if year of birth present; minimum and maximum used for | ||
- | pedigree checks;\\ | + | pedigree checks |
average used to predict year of birth of parent with missing | average used to predict year of birth of parent with missing | ||
pedigree. | pedigree. | ||
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</ | </ | ||
optional\\ | optional\\ | ||
- | if only one sex has records, specifies which parent it is;\\ | + | if only one sex has records, specifies which parent it is |
used for pedigree checks. | used for pedigree checks. | ||
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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 effects (mat, pe and mpe) |
- | this keyword also could be applied to set covariables for fixed effects;\\ | + | |
- | r_type | + | this keyword also could be applied to set covariables for fixed effects; |
- | to be generated from a single data variable; not yet implemented | + | |
+ | //r_type// could be: | ||
+ | * ' | ||
+ | * " | ||
< | < | ||
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r1 .. rq | r1 .. rq | ||
</ | </ | ||
- | for random regressions, | + | for random regressions, |
- | r_type=' | + | |
- | covariable 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=' |
< | < | ||
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</ | </ | ||
- | //g// are (co)variances for the animal effect;\\ | + | //g// are (co)variances for the animal effect |
- | the dimensions of g should account for the maternal | + | |
+ | the dimensions of g should account for random correlated | ||
< | < | ||
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=====Extra comments===== | =====Extra comments===== | ||
- | Sections starting from EFFECTS can be repeated any number of types.\\ | + | Sections starting from EFFECTS can be repeated any number of types. |
If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 | If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 | ||
on diagonals and 0.1 on off-diagonals. | on diagonals and 0.1 on off-diagonals. | ||
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- the default size of character fields | - the default size of character fields | ||
< | < | ||
- | OPTION alpha size nn | + | OPTION alpha size nn |
</ | </ | ||
where //nn// is the new size. | where //nn// is the new size. | ||
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- 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. | ||
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- 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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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 (before elimination due to other effects) | + | 8) number of progenies (before elimination due to other effects) as parent 1 |
- | | + | 9) number of progenies (before elimination due to other effects) as parent 2 |
- | 9) number of progenies (before elimination due to other effects) | + | |
- | | + | |
10) original animal id | 10) original animal id | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani