readme.renumf90
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
readme.renumf90 [2012/05/29 12:24] – [OPTIONS] ignacio | readme.renumf90 [2016/11/04 21:17] – [Additive Pedigree File] shogo | ||
---|---|---|---|
Line 1: | Line 1: | ||
=======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 42: | Line 42: | ||
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 | ||
- | < | + | < |
TRAITS | TRAITS | ||
t1 t2 .. tn | t1 t2 .. tn | ||
Line 76: | Line 76: | ||
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. | ||
Line 87: | Line 89: | ||
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 99: | ||
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 108: | ||
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 120: | ||
</ | </ | ||
- | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only |
+ | |||
+ | //fped// specifies the pedigree file | ||
< | < | ||
Line 120: | Line 129: | ||
</ | </ | ||
- | 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 147: | ||
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]] | ||
Line 144: | Line 163: | ||
</ | </ | ||
- | 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. | ||
< | < | ||
Line 153: | Line 177: | ||
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. | ||
Line 165: | Line 192: | ||
</ | </ | ||
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. | ||
Line 177: | Line 205: | ||
* if t is ' | * if t is ' | ||
- | * if t is ' | + | * if t is ' |
+ | < | ||
+ | INBREEDING | ||
+ | inb_type | ||
+ | </ | ||
+ | optional\\ | ||
+ | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file | ||
+ | |||
+ | // | ||
+ | * ' | ||
+ | * ' | ||
< | < | ||
Line 184: | Line 222: | ||
</ | </ | ||
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;\\ | + | |
- | 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: | ||
+ | * ' | ||
+ | * " | ||
< | < | ||
Line 193: | Line 234: | ||
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 244: | ||
</ | </ | ||
- | //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 | ||
< | < | ||
Line 217: | Line 259: | ||
</ | </ | ||
//gmpe// are (co)variances for the MPE effect if present | //gmpe// are (co)variances for the MPE effect if present | ||
+ | =====Extra comments===== | ||
+ | Sections starting from EFFECTS can be repeated any number of types. | ||
- | =====Extra comments===== | ||
- | |||
- | 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 240: | Line 281: | ||
- 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. | ||
Line 246: | Line 287: | ||
- 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. | ||
Line 252: | Line 293: | ||
- 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. | ||
- | 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 " | ||
Line 290: | Line 336: | ||
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 335: | Line 379: | ||
< | < | ||
# 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