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--- undoc:renumf90 [2016/11/10 03:47] – created yutaka
+++ undoc:renumf90 [2020/04/21 07:04] – yutaka
@@ Line 5: / Line 5: @@
 ==== User-defined UPG code ====
-The program accepts the following keywords in ''UPG_TYPE''.
+By Yutaka Masuda
-    UPG_TYPE
+Renumf90 (version 1.145 or later) supports several methods to assign unknown-parent groups (UPGs) to unknown parents.
-    group
+You can specify the method by ''UPG_TYPE'', which takes one of the following keywords.
-    or
-    UPG_TYPE
-    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's sex (sire or dam), use ''group''. The ''group_unisex'' doesn't consider the sex of parents.
+   * ''yob'': automatic assignment of UPGs based on year-of-birth.
+   * ''in_ped'': use of UPG code (negative integer) embedded in pedigree
+   * ''group_unisex'': manual assignment of UPGs based on user-supplied group code; the same code both for unknown sire and dam.
+   * ''group'': as above; separate UPG code for unknown sire and dam.
+   * ''group_sex'': as above with flexible UPG assignment
-The column in the pedigree file is specified with the 6th item in ''FILE_POS''. The following example tells the program the 5th column in the pedigree file as the group code. The group code will be treated as characters.
+I explain the usage of the last 3 options using the following pedigree file.
+   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 ''0'' for the unknown parent.
+The last 2 columns define groups to which the animal's parents belong.
+You need only 1 group code (either column 4 or 5) with ''group'' and ''group_unisex'', but two groups with ''group_sex''.
+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 ''A1'' and ''A8'' has the same UPG for sire.
+Renumf90 checks the parents of an animal, and if the parent is missing, the program puts a UPG to the missing parents based on the group code of the current animal.
+With ''group_unisex'', renumf90 assigns the same UPG code both to unknown sire and dam.
+For example, in the above pedigree, ''A1'' will have the same UPG code both for its sire and dam.
+With ''group'', you have a separate UPG code for the unknown sire and dam.
+For example, ''A1'' will have two different UPG codes for its parents.
+Put 6th number on ''FILE_POS'' To specify the position of group code in the pedigree file.
+For example, use the following description to specify the 4th column for the groups.
     FILE_POS
-2 3 0 0 5
+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 the unknown dam for ''A1'' and ''A2''.
+It is not possible to do it using the one-group method (''A1'' and ''A2'' share the same group code ''G1'' that will assign the same UPG code to their dams).
+The keyword ''group_sex'' accepts 2 group-columns, and assigns separate UPGs to unknown sire and dam.
+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 ''FILE_POS'' as the 6th and 7th items.
+See the following example.
+    FILE_POS
+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, and renumf90 puts them as unrelated individuals.
+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 ''group_unisex'', and separate UPGs with ''group'' and ''group_sex''.
+You can define the default UPG for such individuals that do not appear in the pedigree file.
+Place ''DEFAULT_GROUP'' just after ''UPG_TYPE'' in the parameter file, and put the group code.
+You need 1 group for ''group_unisex'' and ''group'', and 2 groups for ''group_sex''.
+    # 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 ''FILE_POS''.