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readme.renumf90 [2022/08/08 17:56] – andres | readme.renumf90 [2023/03/02 01:08] – [Options] 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> |
the default is 3 | the default is 3 |
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all pedigrees are loaded if p=0. To consider all ancestors to be traced back from genotyped and phenotyped animals, put a large number like 100. With p=0, RENUMF90 tries to include all animals found in the raw pedigree file even if the animals in the pedigree are not related to the animals with phenotype or genotype. Thus, p=0 is not recommended. | all pedigrees are loaded if p=0. This is the fastest as it reads the pedigree file only once. However, if you want to extract the informative animals (genotyped and phenotyped animals + their ancestors traced back) put a large number like 100. With p=0, RENUMF90 tries to include all animals found in the raw pedigree file even if the animals in the pedigree are not related to the animals with phenotype or genotype. Thus, p=0 is not recommended unless your pedigree file is already prepared and consists in the informative animals or the animals of interest. |
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</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> |
</file> | </file> |
where //nn// is the number of fields. | where //nn// is the number of fields. |
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| <file> |
| OPTION no_basic_statistics |
| </file> |
| avoids the computation of basic statistics (min, max, correlations...) which take a certain time for very large data file. |
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| <file> |
| OPTION inbreeding_method n |
| </file> |
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| allows choosing a method for inbreeding calculation. The inbreeding coefficients are used later (in the other programs) to set up the coefficients for the A-inverse. Existing options are: |
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