readme.renumf90
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readme.renumf90 [2012/05/28 01:01] – created ignacio | readme.renumf90 [2012/05/29 11:42] – ignacio | ||
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- | < | + | |
- | ======================================================= | + | =======RENUMF90====== |
- | RENUMF90 - | + | renumbering program for the BLUPF90 family now works with SNP info\\ |
- | | + | 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 | ||
- | Summary | + | =====Summary===== |
- | ======= | + | |
RENUMF90 is a renumbering program for the BLUPF90 family of programs. It | RENUMF90 is a renumbering program for the BLUPF90 family of programs. It | ||
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Warnings | Warnings | ||
- | - input files cannot contain character #. | + | * input files cannot contain character #. |
- | - missing animals have code 0; 00 may be treated as a known animal | + | |
- | Structure of parameter file | + | =====Structure of parameter file====== |
- | =========================== | + | |
The parameter file contains keywords in capital followed by specifications | The parameter file contains keywords in capital followed by specifications | ||
Line 32: | Line 28: | ||
keywords need to occur sequentially, | keywords need to occur sequentially, | ||
- | Bugs | + | |
- | ==== | + | =====Bugs===== |
IDs starting with " | IDs starting with " | ||
- | Fields in the parameter file | + | |
- | ============================= | + | =====Fields in the parameter file===== |
# Parameter file for program renf90; it is translated to parameter | # Parameter file for program renf90; it is translated to parameter | ||
# file for BLUPF90 family of programs. | # file for BLUPF90 family of programs. | ||
- | Lines with # are treated as comments | + | Lines with # are treated as comments |
| | ||
- | + | < | |
DATAFILE | DATAFILE | ||
f1 | f1 | ||
+ | </ | ||
+ | The data file is f1 | ||
- | The data file is f1 | + | <file> |
TRAITS | TRAITS | ||
t1 t2 .. tn | t1 t2 .. tn | ||
+ | </ | ||
+ | t1-tn are positions of traits in datafile; n defines the number of traits | ||
- | t1-tn are positions of traits in datafile; n defines the number of traits | + | < |
- | + | ||
FIELDS_PASSED TO OUTPUT | FIELDS_PASSED TO OUTPUT | ||
p1 p2 .. pm | p1 p2 .. pm | ||
- | + | < | |
- | | + | fields p1-pn are passed to output without changes; can be empty |
+ | < | ||
WEIGHT(S) | WEIGHT(S) | ||
w | w | ||
- | w is position of weight if present; can be empty | + | </ |
- | + | w is position of weight if present; can be empty | |
+ | |||
+ | < | ||
RESIDUAL_VARIANCE | RESIDUAL_VARIANCE | ||
r | r | ||
- | r is matrix of residual (co)variances | + | </ |
+ | r is matrix of residual (co)variances | ||
+ | < | ||
EFFECT | EFFECT | ||
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; positions can be different for each trait for fixed | ||
+ | effects; for random effects, only one position + 0 (misising) efefct are | ||
+ | possible. | ||
+ | * type is ' | ||
+ | * form is ' | ||
- | this line defines one group of effects; e1 .. en are positions of this | + | < |
- | | + | |
- | | + | |
- | | + | |
- | + | ||
- | type is ' | + | |
- | + | ||
- | form is ' | + | |
NESTED | NESTED | ||
d1 .. dn form | d1 .. dn form | ||
- | + | </ | |
- | | + | optional for covariables only, specifies nesting; form is as above |
| | ||
+ | < | ||
RANDOM | RANDOM | ||
rtype | rtype | ||
+ | </ | ||
- | the RANDOM keyword occurs only if the current effect is random; | + | the RANDOM keyword occurs only if the current effect is random; |
- | | + | rtype is ' |
- | + | ||
+ | < | ||
OPTIONAL | OPTIONAL | ||
o1 o2.. oq | o1 o2.. oq | ||
+ | < | ||
+ | causes extra effects appended to the animal effect; current options include | ||
+ | ' | ||
+ | permanent environment | ||
- | | + | < |
- | ' | + | |
- | | + | |
- | + | ||
FILE | FILE | ||
fped | fped | ||
+ | </ | ||
- | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only, fped specifies the pedigree file |
+ | < | ||
FILE_POS | FILE_POS | ||
an s d alt_dam yob | an s d alt_dam yob | ||
+ | </ | ||
- | for animal effect only; specifies positions in the pedigree file of animal | + | 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; 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. |
+ | < | ||
SNP_FILE | SNP_FILE | ||
fsnp | fsnp | ||
+ | </ | ||
- | optional; fsnp specifies files with ID and SNP information; | + | optional; fsnp specifies files with ID and SNP information; |
- | | + | relationship matrix will be constructed as in Aguilar et al. (2010) and will |
- | | + | include the genomic information; |
- | | + | 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 PreGSf90 |
- | + | < | |
PED_DEPTH | PED_DEPTH | ||
p | p | ||
- | + | </ | |
- | | + | |
- | | + | optional for animal effect only; p specifies the depth of pedigree search; |
- | | + | the default is 3; all pedigrees are loaded if p=0. |
+ | |||
+ | < | ||
GEN_INT | GEN_INT | ||
min avg max | min avg max | ||
+ | </ | ||
+ | optional; specifies minimum, average and maximum generation interval; | ||
+ | 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. | ||
- | optional; specifies minimum, average and maximum generation interval; | + | < |
- | | + | |
- | | + | |
- | | + | |
- | + | ||
REC_SEX | REC_SEX | ||
i | i | ||
+ | </ | ||
+ | optional; if only one sex has records, specifies which parent it is; used for | ||
+ | pedigree checks. | ||
- | optional; if only one sex has records, specifies which parent it is; used for | + | < |
- | | + | |
- | + | ||
UPG_TYPE | UPG_TYPE | ||
t | t | ||
- | + | </ | |
- | | + | 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, |
- | + | < | |
RANDOM_REGRESSION | RANDOM_REGRESSION | ||
r_type | r_type | ||
+ | </ | ||
+ | Specifies that random regressions should be applied to the animal and | ||
+ | corresponding effects (mat, pe and mpe), this keyword also could be | ||
+ | applied to set covariables for fixed effects; r_type is ' | ||
+ | random regressions are in the data, or " | ||
+ | to be generated from a single data variable; not yet implemented | ||
- | Specifies that random regressions should be applied to the animal and | + | < |
- | | + | |
- | | + | |
- | | + | |
- | to be generated from a single data variable; not yet implemented | + | |
- | + | ||
RR_POSITION | RR_POSITION | ||
r1 .. rq | r1 .. rq | ||
- | for random regressions, | + | </ |
- | | + | for random regressions, |
- | | + | r_type=' |
- | | + | covariable if r_type=' |
+ | </ | ||
+ | |||
+ | < | ||
(CO)VARIANCES | (CO)VARIANCES | ||
g | g | ||
+ | </ | ||
- | g are (co)variances for the animal effect; the dimensions of g should | + | //g// are (co)variances for the animal effect; the dimensions of g should |
- | | + | account for the maternal effect if present |
- | | + | |
+ | < | ||
(CO)VARIANCES_PE | (CO)VARIANCES_PE | ||
gpe | gpe | ||
+ | </ | ||
+ | //gpe// are (co)variances for the PE effect if present | ||
- | gpe are (co)variances for the PE effect if present | + | < |
(CO)VARIANCES_MPE | (CO)VARIANCES_MPE | ||
gmpe | gmpe | ||
- | + | </ | |
- | | + | //gmpe// are (co)variances for the MPE effect if present |
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yy 2 2 | yy 2 2 | ||
zz 2 3 | zz 2 3 | ||
- | <\file> | + | </file> |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani