readme.renumf90
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readme.renumf90 [2012/05/29 11:50] – ignacio | readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio | ||
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The parameter file contains keywords in capital followed by specifications | The parameter file contains keywords in capital followed by specifications | ||
- | of a given effect/data item. The keywords need to be typed exactly. Specific | + | of a given effect/data item.\\ The keywords need to be typed exactly.\\ Specific |
keywords need to occur sequentially, | keywords need to occur sequentially, | ||
Line 42: | Line 42: | ||
Lines with # are treated as comments | Lines with # are treated as comments | ||
| | ||
- | < | + | < |
DATAFILE | DATAFILE | ||
f1 | f1 | ||
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The data file is f1 | The data file is f1 | ||
- | < | + | < |
TRAITS | TRAITS | ||
t1 t2 .. tn | t1 t2 .. tn | ||
Line 66: | Line 66: | ||
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 | ||
Line 97: | Line 97: | ||
rtype is ' | rtype is ' | ||
- | < | + | < |
OPTIONAL | OPTIONAL | ||
o1 o2.. oq | o1 o2.. oq | ||
Line 105: | Line 105: | ||
permanent environment | permanent environment | ||
- | < | + | < |
FILE | FILE | ||
fped | fped | ||
Line 125: | Line 125: | ||
dam. | dam. | ||
- | < | + | < |
SNP_FILE | SNP_FILE | ||
fsnp | fsnp | ||
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include digits 0, 1, 2 and 5; ID and SNP info need to be separated by | 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 | at leats one space; see info for program PreGSf90 | ||
- | < | + | |
+ | < | ||
PED_DEPTH | PED_DEPTH | ||
p | p | ||
Line 144: | Line 145: | ||
the default is 3; all pedigrees are loaded if p=0. | the default is 3; all pedigrees are loaded if p=0. | ||
- | < | + | < |
GEN_INT | GEN_INT | ||
min avg max | min avg max | ||
Line 153: | Line 154: | ||
pedigree. | pedigree. | ||
- | < | + | < |
REC_SEX | REC_SEX | ||
i | i | ||
Line 160: | Line 161: | ||
pedigree checks. | pedigree checks. | ||
- | < | + | < |
UPG_TYPE | UPG_TYPE | ||
t | t | ||
Line 176: | Line 177: | ||
custom_upg(year_of_birth, | custom_upg(year_of_birth, | ||
- | < | + | < |
RANDOM_REGRESSION | RANDOM_REGRESSION | ||
r_type | r_type | ||
Line 186: | Line 187: | ||
to be generated from a single data variable; not yet implemented | to be generated from a single data variable; not yet implemented | ||
- | < | + | < |
RR_POSITION | RR_POSITION | ||
r1 .. rq | r1 .. rq | ||
Line 195: | Line 196: | ||
</ | </ | ||
- | < | + | < |
(CO)VARIANCES | (CO)VARIANCES | ||
g | g | ||
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account for the maternal effect if present | account for the maternal effect if present | ||
- | < | + | < |
(CO)VARIANCES_PE | (CO)VARIANCES_PE | ||
gpe | gpe | ||
Line 209: | Line 210: | ||
//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 | ||
Line 303: | Line 304: | ||
=====Example====== | =====Example====== | ||
+ | |||
+ | |||
+ | **__data file__** - '' | ||
< | < | ||
- | data file - data.test | ||
- | --------------------- | ||
1 aa 34.5 11 12 zz | 1 aa 34.5 11 12 zz | ||
3 bb 21.333 22 23 xx | 3 bb 21.333 22 23 xx | ||
Line 315: | Line 317: | ||
</ | </ | ||
+ | |||
+ | **__pedigree file__** - '' | ||
< | < | ||
- | pedigree file - test.ped | ||
- | ------------------------ | ||
qq 0 0 | qq 0 0 | ||
aa 0 0 | aa 0 0 | ||
Line 325: | Line 327: | ||
</ | </ | ||
- | </ | + | |
- | parameter file - testpar1 | + | **__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 f programs. | # file for BLUPF90 family f programs. | ||
Line 372: | Line 374: | ||
</ | </ | ||
- | </ | + | **__printout__** \\ |
- | printout | + | \\ |
- | ------------------------------------------------------ | + | (temporary; the amount of details may change) |
+ | < | ||
| | ||
name of parameter file? testpar1 | name of parameter file? testpar1 | ||
Line 465: | Line 468: | ||
</ | </ | ||
+ | **__new parameter file__** - '' | ||
< | < | ||
- | new parameter file - renf90.par | ||
- | ------------------------------- | ||
# BLUPF90 parameter file created by RENF90 | # BLUPF90 parameter file created by RENF90 | ||
DATAFILE | DATAFILE | ||
Line 531: | Line 533: | ||
+ | |||
+ | **__data file__** - '' | ||
< | < | ||
- | data file - renf90.dat | ||
- | ---------------------- | ||
34.5 11 1 3 5 12 1 3 aa 1 | 34.5 11 1 3 5 12 1 3 aa 1 | ||
| | ||
Line 542: | Line 544: | ||
</ | </ | ||
+ | |||
+ | **__Pedigree file__** - '' | ||
< | < | ||
- | | ||
- | | ||
1 6 3 1 0 2 2 0 0 bb | 1 6 3 1 0 2 2 0 0 bb | ||
6 0 0 1 0 0 0 2 0 qq | 6 0 0 1 0 0 0 2 0 qq | ||
Line 554: | Line 556: | ||
</ | </ | ||
+ | **'' | ||
< | < | ||
- | renumbering tables - renf90.tables | ||
- | ---------------------------------- | ||
| | ||
| |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani