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 11:55] – ignacio | readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio | ||
---|---|---|---|
Line 25: | Line 25: | ||
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 | ||
Line 48: | Line 48: | ||
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 | ||
Line 136: | Line 136: | ||
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 | ||
Line 203: | Line 204: | ||
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 305: | Line 306: | ||
- | ===data file - data.test=== | + | **__data file__** |
< | < | ||
Line 317: | Line 318: | ||
- | ===pedigree file - test.ped=== | + | **__pedigree file__** |
< | < | ||
qq 0 0 | qq 0 0 | ||
Line 327: | Line 328: | ||
- | ===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 | ||
Line 373: | Line 374: | ||
</ | </ | ||
- | ===printout | + | **__printout__** \\ |
+ | \\ | ||
+ | (temporary; the amount of details may change) | ||
< | < | ||
| | ||
Line 465: | Line 468: | ||
</ | </ | ||
- | ===new | + | **__new |
< | < | ||
# BLUPF90 parameter file created by RENF90 | # BLUPF90 parameter file created by RENF90 | ||
Line 531: | Line 534: | ||
- | ===data file - renf90.dat=== | + | **__data file__** |
< | < | ||
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 545: | ||
- | ===Pedigree file (same format as from renum) | + | **__Pedigree file__** |
< | < | ||
1 6 3 1 0 2 2 0 0 bb | 1 6 3 1 0 2 2 0 0 bb | ||
Line 553: | Line 556: | ||
</ | </ | ||
- | ===renumbering tables - renf90.tables=== | + | **'' |
< | < | ||
| |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani