readme.renumf90
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readme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio | readme.renumf90 [2023/06/12 16:47] – [Options] 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 | ||
Line 21: | Line 21: | ||
* 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 38: | ||
=====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 |
< | < | ||
Line 76: | Line 82: | ||
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;\\ | + | |
- | for random effects, only one position + 0 (misising) efefct are | + | positions can be different for each trait for fixed effects; |
+ | |||
+ | for random effects, only one position + 0 (missing) efefct are | ||
possible. | possible. | ||
* type is ' | * type is ' | ||
- | * form is ' | + | * for crossclassified effects: |
+ | * for covariables: | ||
< | < | ||
Line 87: | Line 96: | ||
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 | ||
| | ||
Line 96: | Line 106: | ||
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: |
+ | * ' | ||
+ | * ' | ||
+ | * ' | ||
< | < | ||
Line 102: | Line 115: | ||
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: | ||
* ' | * ' | ||
* ' | * ' | ||
- | * ' | + | * ' |
< | < | ||
Line 113: | Line 127: | ||
</ | </ | ||
- | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only |
+ | |||
+ | //fped// specifies the pedigree file | ||
+ | |||
+ | < | ||
+ | SKIP_HEADER | ||
+ | n | ||
+ | </ | ||
+ | This is optional. It skips the first n lines as header in the pedigree file. | ||
< | < | ||
Line 120: | Line 142: | ||
</ | </ | ||
- | for animal effect only;\\ | + | for animal effect only; |
- | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam | + | |
- | missing alt_dam or yob can be replaced by 0\\ | + | specifies positions in the pedigree file of animal |
- | 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. | + | 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. | ||
< | < | ||
Line 132: | Line 160: | ||
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 for animal effect only; p specifies the depth of pedigree search; | + | optional |
- | the default is 3; all pedigrees are loaded if p=0. | + | |
+ | for animal effect only; | ||
+ | |||
+ | //p// specifies the depth of pedigree search; | ||
+ | |||
+ | the default is 3 | ||
+ | |||
+ | 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 151: | Line 191: | ||
min avg max | min avg max | ||
</ | </ | ||
- | optional; specifies minimum, average and maximum generation interval; | + | optional |
+ | |||
+ | 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; average used to predict year of birth of parent with missing | + | pedigree checks |
+ | |||
+ | average used to predict year of birth of parent with missing | ||
pedigree. | pedigree. | ||
Line 160: | Line 205: | ||
i | i | ||
</ | </ | ||
- | optional; if only one sex has records, specifies which parent it is; used for | + | optional\\ |
- | pedigree checks. | + | if only one sex has records, specifies which parent it is |
+ | |||
+ | used for pedigree checks. | ||
< | < | ||
Line 167: | Line 214: | ||
t | t | ||
</ | </ | ||
- | optional; | + | optional\\ |
- | if t is ' | + | |
- | subsequent line should contain list of years to separate different UPG; | + | |
- | if t is ' | + | * if t is ' |
- | UPG number that this missing parent should be allocated to; in this option, | + | |
- | all known parents should have pedigree lines, i.e., each parent field should | + | |
- | contain either the ID of a real parent, or a negative UPG number. | + | |
- | if t is ' | + | * if t is ' |
- | custom_upg(year_of_birth, | + | |
+ | * 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 '' | ||
< | < | ||
Line 184: | Line 247: | ||
</ | </ | ||
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), this keyword also could be | + | corresponding |
- | applied to set covariables for fixed effects; r_type | + | |
- | random regressions are in the data, or " | + | this keyword also could be applied to set covariables for fixed effects; |
- | to be generated from a single data variable; | + | |
+ | //r_type// could be: | ||
+ | * ' | ||
+ | * " | ||
< | < | ||
Line 193: | Line 259: | ||
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=' |
< | < | ||
Line 203: | Line 269: | ||
</ | </ | ||
- | //g// are (co)variances for the animal effect; the dimensions of g should | + | //g// are (co)variances for the animal effect |
- | account for the maternal | + | |
+ | the dimensions of g should account for random correlated | ||
< | < | ||
Line 219: | Line 286: | ||
- | ---- | + | ==== 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===== | ||
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. | ||
Line 230: | Line 321: | ||
The sequence of keywords should be as above although optional fields can be | The sequence of keywords should be as above although optional fields can be | ||
- | skipped. Keywords out of order may not be recognized. | + | skipped. |
- | =====OPTIONS===== | + | Keywords out of order may not be recognized. |
+ | |||
+ | =====Options===== | ||
The following options can added at the end of the parameter file to redefine | The following options can added at the end of the parameter file to redefine | ||
- | parameter | + | parameters |
- | - 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 | + | - the maximum |
< | < | ||
- | | + | OPTION max_field_readline nn |
</ | </ | ||
- | where nn is the number of fields. | + | where //nn// is the number of fields. |
+ | < | ||
+ | OPTION missing x | ||
+ | </ | ||
+ | |||
+ | allows indicating that missing value is the number x (e.g. 999) for instance if 0 is a valid record. | ||
+ | |||
+ | < | ||
+ | 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 RENUMF90 can contain many lines beginning with OPTION. | + | 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 parameter file renf90.par to be used by application programs. |
=====Combining fields or interactions====== | =====Combining fields or interactions====== | ||
- | Several fields in the data file can be combined into one using a COMBINE keyword. | + | Several fields in the data file can be combined into one using a '' |
< | < | ||
COMBINE a b c .... | COMBINE a b c .... | ||
</ | </ | ||
- | catenates b c ... into c. Keywords | + | catenates |
- | file, but possibly after comments. There may be many combined fields. | + | Keyword |
+ | |||
+ | There may be many combined fields. | ||
For example: | For example: | ||
- | </file> | + | < |
COMBINE 7 2 3 4 | COMBINE 7 2 3 4 | ||
</ | </ | ||
- | combines content of fields 2 3 4 into field 7; the data file is not changed, | + | |
- | only the program treats field 7 as fields 2 3 4 put together (without spaces). | + | combines content of fields 2 3 4 into field 7; |
- | The combined fields can be treated as " | + | |
- | and if their total length is <9. Otherwise, they need to be used as " | + | the data file is not changed, only the program treats field 7 as fields 2 3 4 put together (without spaces). |
- | Please note that the maximum size of the combined variable is limited by the | + | |
- | largest size of the " | + | |
+ | The combined fields can be treated as " | ||
+ | |||
+ | Please note that the maximum size of the combined variable is limited by the largest size of the " | ||
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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 | + | 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 333: | Line 461: | ||
< | < | ||
# 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