undoc:renumf90
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undoc:renumf90 [2016/11/10 03:47] – created yutaka | undoc:renumf90 [2020/04/21 07:00] – yutaka | ||
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==== User-defined UPG code ==== | ==== User-defined UPG code ==== | ||
- | The program accepts the following keywords in '' | + | By Yutaka Masuda |
- | UPG_TYPE | + | Renumf90 (version 1.145 or later) supports several methods to assign unknown-parent groups (UPGs) to missing parents. |
- | group | + | You can specify the method by '' |
- | + | ||
- | | + | |
- | + | ||
- | | + | |
- | group_unisex | + | |
- | With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns an UPG code according to the group code. If you want to assign separate UPGs by the parent' | + | * '' |
+ | * '' | ||
+ | * '' | ||
+ | | ||
+ | | ||
- | The column in the pedigree file is specified with the 6th item in '' | + | I explain |
+ | |||
+ | A1 0 0 G1 H1 | ||
+ | A2 0 0 G1 H2 | ||
+ | A3 A2 A1 G2 H1 | ||
+ | A4 A3 0 G1 H1 | ||
+ | A5 0 A4 G2 H2 | ||
+ | A6 A5 A4 G2 H2 | ||
+ | A7 A5 A4 G1 H1 | ||
+ | A8 0 A7 G1 H1 | ||
+ | A9 A8 0 G2 H2 | ||
+ | |||
+ | 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' | ||
+ | You need only 1 group code (either column 4 or 5) with '' | ||
+ | The group code can include any characters. | ||
+ | |||
+ | ===== With one group code ===== | ||
+ | |||
+ | Renumf90 assumes that the animals with the same group-code have a common UPG. | ||
+ | For example, with the group code in column 4, animal '' | ||
+ | Renumf90 checks the parents of an animal, and if the parent is missing, | ||
+ | |||
+ | With '' | ||
+ | For example | ||
+ | |||
+ | With '' | ||
+ | For example, '' | ||
+ | |||
+ | Put 6th number on '' | ||
+ | For example, use the following description to specify the 4th column for the groups. | ||
FILE_POS | FILE_POS | ||
- | 1 2 3 0 0 5 | + | 1 2 3 0 0 4 |
+ | |||
+ | ===== With two group code ===== | ||
+ | |||
+ | There is a case you need more flexibility. | ||
+ | For example, you may want to assign a separate UPG code to missing dam for '' | ||
+ | It is not possible to do it using one-group method ('' | ||
+ | |||
+ | The keyword '' | ||
+ | If the sire is missing, renumf90 assigns a UPG code based on the 1st group column, and for missing dams, the 2nd group column. | ||
+ | You should put the positions of the group columns in '' | ||
+ | See the following example. | ||
+ | |||
+ | FILE_POS | ||
+ | 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 | ||
- | The program now accept 3 items, 5 items, or 6 items in '' | ||
undoc/renumf90.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1