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readme.renumf90 [2022/05/05 19:02] – [Summary] dani | readme.renumf90 [2023/01/25 12:46] – [Fields in the parameter file] andres |
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<file> | <file> |
WEIGHT(S) | WEIGHT(S) |
w | w1 [w2 w3...wn] |
</file> | </file> |
w is position of weight if present; can be empty | w1 [w2 w3...wn] are position of weight(s) if present; can be empty (which means weight of 1 or no weight). Either there is a single weight, the same for all traits, or one weight per trait in which case ''ntrait'' positions are needed in this line. See [[readme.blupf90plus#weights|blupf90+ section on WEIGHTS]] for details. |
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<file> | <file> |
positions can be different for each trait for fixed effects; | positions can be different for each trait for fixed effects; |
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for random effects, only one position + 0 (misising) efefct are | for random effects, only one position + 0 (missing) efefct are |
possible. | possible. |
* type is 'cross' for crossclassified or 'cov' for covariables | * type is 'cross' for crossclassified or 'cov' for covariables |
* form is 'alpha' for alphanumeric or 'numer' for numeric | * for crossclassified effects: form is 'alpha' for alphanumeric or 'numer' for numeric |
| * for covariables: neither 'alpha' nor 'numer' are needed; don't put anything after 'cov' |
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<file> | <file> |
</file> | </file> |
optional\\ | optional\\ |
use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file. Inbreeding calculation is a default in RENUMF90 ≥ v1.157, even if this keyword is not used. |
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//inb_type// could be: | //inb_type// could be: |
* 'pedigree' - the program computes inbreeding coefficients with Meuwissen and Luo (1992) using the pedigree to be saved in renaddxx.ped; calculated inbreeding coefficients will be saved in a file "renf90.inb" with the original ID | * 'pedigree' - the program computes inbreeding coefficients with Meuwissen and Luo (1992) using the pedigree to be saved in renaddxx.ped; calculated inbreeding coefficients will be saved in a file "renf90.inb" with the original ID |
* 'file' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. The file has at least 2 columns: original_ID and inbreeding value (from 0.0 to 1.0). The program just skips unnecessary IDs | * 'file' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. The file has at least 2 columns: original_ID and inbreeding value (from 0.0 to 1.0). The program just skips unnecessary IDs |
| * 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation |
| * 'no-inbreeding' - turn inbreeding calculation off in RENUMF90 ≥ v1.157 |
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<file> | <file> |