readme.renumf90
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| readme.renumf90 [2012/05/29 11:33] – ignacio | readme.renumf90 [2012/05/29 11:36] – ignacio | ||
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| Line 33: | Line 33: | ||
| 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 | ||
| Line 43: | Line 42: | ||
| 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 | ||
| | | ||
| Line 80: | Line 85: | ||
| 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 | ||
| Line 114: | Line 127: | ||
| dam. | dam. | ||
| + | < | ||
| SNP_FILE | SNP_FILE | ||
| fsnp | fsnp | ||
| + | </ | ||
| | | ||
| Line 123: | Line 138: | ||
| | | ||
| 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