readme.renumf90
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| readme.renumf90 [2012/05/29 12:07] – [Structure of parameter file] ignacio | readme.renumf90 [2012/05/29 12:14] – [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 76: | Line 76: | ||
| 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 effect for all traits;\\ |
| - | effect for all traits; positions can be different for each trait for fixed | + | positions can be different for each trait for fixed effects;\\ |
| - | effects; for random effects, only one position + 0 (misising) efefct are | + | for random effects, only one position + 0 (misising) efefct are |
| possible. | possible. | ||
| * type is ' | * type is ' | ||
| Line 87: | Line 87: | ||
| d1 .. dn form | d1 .. dn form | ||
| </ | </ | ||
| - | optional for covariables only, specifies nesting; form is as above | + | optional for covariables only, specifies nesting;\\ |
| + | form is as above | ||
| | | ||
| < | < | ||
| Line 97: | Line 98: | ||
| rtype is ' | rtype is ' | ||
| - | < | + | < |
| OPTIONAL | OPTIONAL | ||
| o1 o2.. oq | o1 o2.. oq | ||
| </ | </ | ||
| - | causes extra effects appended to the animal effect; current options include | + | causes extra effects appended to the animal effect;\\ |
| - | ' | + | current options include |
| - | permanent environment | + | |
| + | * ' | ||
| + | * 'mpe' for maternal permanent environment | ||
| - | < | + | < |
| FILE | FILE | ||
| fped | fped | ||
| Line 117: | Line 120: | ||
| </ | </ | ||
| - | for animal effect only; specifies positions in the pedigree file of animal | + | for animal effect only;\\ |
| - | an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing | + | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ |
| - | alt_dam or yob can be replaced by 0; if this line is not given, defaults are | + | missing alt_dam or yob can be replaced by 0\\ |
| - | 1 2 3 0 0. If maternal effect is specified, the maternal effect is due to | + | if this line is not given, defaults are 1 2 3 0 0.\\ |
| - | position of d if alt_dam field is 0, or otherwise is due to alt_dam; If | + | 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. |
| - | 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;\\ |
| - | relationship matrix will be constructed as in Aguilar et al. (2010) and will | + | //fsnp// specifies files with ID and SNP information; |
| - | include the genomic information; | + | if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will |
| - | same format as fped and SNP info needs to start from a fixed column and | + | include the genomic information; |
| - | include digits 0, 1, 2 and 5; ID and SNP info need to be separated by | + | file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and |
| - | at leats one space; see info for program PreGSf90 | + | include digits 0, 1, 2 and 5;\\ |
| - | < | + | ID and SNP info need to be separated by at leats one space; see info for program |
| + | |||
| + | < | ||
| PED_DEPTH | PED_DEPTH | ||
| p | p | ||
| Line 144: | Line 147: | ||
| 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 156: | ||
| pedigree. | pedigree. | ||
| - | < | + | < |
| REC_SEX | REC_SEX | ||
| i | i | ||
| Line 160: | Line 163: | ||
| pedigree checks. | pedigree checks. | ||
| - | < | + | < |
| UPG_TYPE | UPG_TYPE | ||
| t | t | ||
| Line 176: | Line 179: | ||
| custom_upg(year_of_birth, | custom_upg(year_of_birth, | ||
| - | < | + | < |
| RANDOM_REGRESSION | RANDOM_REGRESSION | ||
| r_type | r_type | ||
| Line 186: | Line 189: | ||
| 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 198: | ||
| </ | </ | ||
| - | < | + | < |
| (CO)VARIANCES | (CO)VARIANCES | ||
| g | g | ||
| Line 203: | Line 206: | ||
| 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 212: | ||
| //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