readme.renumf90
Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revision | Next revisionBoth sides next revision | ||
| readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio | readme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio | ||
|---|---|---|---|
| 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 101: | Line 102: | ||
| 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 | ||
| < | < | ||
| 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. | + | |
| < | < | ||
| Line 130: | Line 131: | ||
| </ | </ | ||
| - | 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 | ||
| < | < | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani