readme.renumf90
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readme.renumf90 [2012/05/28 01:02] – ignacio | readme.renumf90 [2012/05/29 11:36] – 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 | ||
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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 | ||
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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 | ||
+ | < | ||
| | ||
+ | < | ||
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 | this line defines one group of effects; e1 .. en are positions of this | ||
| | ||
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form is ' | form is ' | ||
+ | < | ||
NESTED | NESTED | ||
d1 .. dn form | d1 .. dn form | ||
+ | </ | ||
| | ||
| | ||
+ | < | ||
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 ' | rtype is ' | ||
- | + | ||
+ | < | ||
OPTIONAL | OPTIONAL | ||
o1 o2.. oq | o1 o2.. oq | ||
+ | < | ||
| | ||
' | ' | ||
| | ||
- | | + | |
+ | < | ||
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 | ||
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dam. | dam. | ||
+ | < | ||
SNP_FILE | SNP_FILE | ||
fsnp | fsnp | ||
+ | </ | ||
| | ||
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| | ||
at leats one space; see info for program PreGSf90 | at leats one space; see info for program PreGSf90 | ||
- | + | < | |
PED_DEPTH | PED_DEPTH | ||
p | p | ||
- | + | </ | |
+ | |||
+ | < | ||
| | ||
the default is 3; all pedigrees are loaded if p=0. | the default is 3; all pedigrees are loaded if p=0. |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani