undoc:renumf90
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undoc:renumf90 [2020/04/21 06:46] – yutaka | undoc:renumf90 [2020/04/21 07:04] – yutaka | ||
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By Yutaka Masuda | By Yutaka Masuda | ||
- | Renumf90 (version 1.145 or later) supports several methods to assign unknown-parent groups (UPGs) to missing | + | Renumf90 (version 1.145 or later) supports several methods to assign unknown-parent groups (UPGs) to unknown |
You can specify the method by '' | You can specify the method by '' | ||
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The first 3 columns store the pre-renumbering pedigree (animal, sire, and dam), and the pedigree should have '' | The first 3 columns store the pre-renumbering pedigree (animal, sire, and dam), and the pedigree should have '' | ||
- | The last 2 columns define groups to that the animal' | + | The last 2 columns define groups to which the animal' |
You need only 1 group code (either column 4 or 5) with '' | You need only 1 group code (either column 4 or 5) with '' | ||
+ | The group code can include any characters. | ||
===== With one group code ===== | ===== With one group code ===== | ||
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With '' | With '' | ||
- | For example in the above pedigree, '' | + | For example, in the above pedigree, '' |
With '' | With '' | ||
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There is a case you need more flexibility. | There is a case you need more flexibility. | ||
- | For example, you may want to assign a separate UPG code to missing | + | For example, you may want to assign a separate UPG code to the unknown |
- | It is not possible to do it using one-group method ('' | + | It is not possible to do it using the one-group method ('' |
The keyword '' | The keyword '' | ||
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FILE_POS | FILE_POS | ||
1 2 3 0 0 4 5 | 1 2 3 0 0 4 5 | ||
+ | |||
+ | ===== Default UPG ===== | ||
+ | |||
+ | There may be animals that are not in the pedigree file. | ||
+ | For example, some genotyped animals have no pedigree information, | ||
+ | Such additional individuals have missing parents, that should be replaced by UPGs. | ||
+ | Because those individuals are not in pedigree and renumf90 does not know which UPGs are suitable, the program assigns a separate UPG code to their parents by default; the same UPG will be assigned for both parents with '' | ||
+ | |||
+ | You can define the default UPG for such individuals that do not appear in the pedigree file. | ||
+ | Place '' | ||
+ | You need 1 group for '' | ||
+ | |||
+ | # for group | ||
+ | UPG_TYPE | ||
+ | group | ||
+ | DEFAULT_GROUP | ||
+ | G1 | ||
+ | | ||
+ | # for group_sex | ||
+ | UPG_TYPE | ||
+ | group_sex | ||
+ | DEFAULT_GROUP | ||
+ | G1 H1 | ||
undoc/renumf90.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1