readme.renumf90
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| readme.renumf90 [2012/05/29 11:36] – ignacio | readme.renumf90 [2012/05/29 11:39] – ignacio | ||
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| # file for BLUPF90 family of programs. | # file for BLUPF90 family of programs. | ||
| - | Lines with # are treated as comments | + | Lines with # are treated as comments |
| | | ||
| < | < | ||
| Line 46: | Line 46: | ||
| f1 | f1 | ||
| </ | </ | ||
| - | The data file is f1 | + | The data file is f1 |
| < | < | ||
| Line 52: | Line 52: | ||
| 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 |
| < | < | ||
| Line 58: | Line 58: | ||
| p1 p2 .. pm | p1 p2 .. pm | ||
| < | < | ||
| - | fields p1-pn are passed to output without changes; can be empty | + | fields p1-pn are passed to output without changes; can be empty |
| < | < | ||
| Line 64: | Line 64: | ||
| w | w | ||
| </ | </ | ||
| - | w is position of weight if present; can be empty | + | w is position of weight if present; can be empty |
| < | < | ||
| Line 70: | Line 70: | ||
| r | r | ||
| </ | </ | ||
| - | r is matrix of residual (co)variances | + | r is matrix of residual (co)variances |
| < | < | ||
| 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; positions can be different for each trait for fixed |
| - | | + | effects; for random effects, only one position + 0 (misising) efefct are |
| - | | + | possible. |
| - | + | | |
| - | type is ' | + | |
| - | + | ||
| - | form is ' | + | |
| < | < | ||
| Line 89: | 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 96: | Line 94: | ||
| </ | </ | ||
| - | the RANDOM keyword occurs only if the current effect is random; | + | the RANDOM keyword occurs only if the current effect is random; |
| - | | + | rtype is ' |
| < | < | ||
| Line 103: | Line 101: | ||
| 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 |
| < | < | ||
| Line 112: | Line 110: | ||
| </ | </ | ||
| - | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only, fped specifies the pedigree file |
| < | < | ||
| Line 119: | Line 117: | ||
| </ | </ | ||
| - | for animal effect only; specifies positions in the pedigree file of animal | + | for animal effect only; specifies positions in the pedigree file of animal |
| - | | + | an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing |
| - | | + | alt_dam or yob can be replaced by 0; if this line is not given, defaults are |
| - | | + | 1 2 3 0 0. 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. |
| < | < | ||
| Line 132: | Line 130: | ||
| </ | </ | ||
| - | optional; fsnp specifies files with ID and SNP information; | + | optional; fsnp specifies files with ID and SNP information; |
| - | | + | relationship matrix will be constructed as in Aguilar et al. (2010) and will |
| - | | + | include the genomic information; |
| - | | + | same format as fped and SNP info needs to start from a fixed column and |
| - | | + | 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 |
| < | < | ||
| PED_DEPTH | PED_DEPTH | ||
| Line 144: | Line 142: | ||
| < | < | ||
| - | optional for animal effect only; p specifies the depth of pedigree search; | + | optional for animal effect only; p specifies the depth of pedigree search; |
| - | | + | the default is 3; all pedigrees are loaded if p=0. |
| GEN_INT | GEN_INT | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani