readme.renumf90
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| readme.renumf90 [2012/05/29 12:07] – [Structure of parameter file] ignacio | readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio | ||
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| 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 | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani