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title: Data preparation with RENUMF90 author: Andres Legarra date: September 2019 subject: "Introduction to BLUPF90 suite programs" tags: [introduction,tutorial] ...

What if I don't want to use RENUMF90?

It happens that the user does not want to use RENUMF90. Common reasons for this are:

  • It is simulated data and it is already renumbered
  • I do my own renumbering and I want to use it
  • I have a complex model and I want better control on the recorded numbers

In the next section, we will give instructions on how the files should be coded. We will not give software but you may take a look here.

Main requirements of recoding for BLUPF90 programs

  • Levels of effects should be coded with consecutive numbers. The order may be "natural" or not. For instance, if years in data are (2010, 2011, 2013, 2014) may be renumbered as (1,2,3,4) or (2,1,3,4).
  • The animal is another effect, so it has receive codes from 1 to the number of animals in the pedigree file (this is usually greater than the number of animals in the data file).
  • The animal effect does not need to be renumbered in consecutive order (parents before offspring), but this order is a correct one and may be used. So, for instance, this renumbering is correct:
  A 0 0
  B 0 0
  D A B
  E A D
  F B E
  Z A B

could be recoded as

1 0 0 A 0 0
2 0 0 B 0 0
3 1 2 D A B
4 1 2 Z A B
5 1 3 E A D
6 2 5 F B E

(the last three columns are not needed but help the visualization).

Unknown parent groups

However, if unknown parent groups (UPGs) are in the pedigree, things get more complicated. Assume that we have $n$ real animals and $m$ UPGs. Animals have to be renumbered with codes from 1 to $n$, and UPGs have to be renumbered with codes from $n+1$ to $n+m$. In addition, because they do not have ancestors, the UPGs must not have a line on their own in the pedigree file for BLUPF90. In that way, BLUPF90 "knows" that a given number is a UPG and not an individual. For instance, in the previous example assume that UPGs are "unknown2000" and "unknown2004":

  A unknown2000 unknown2000
  B unknown2000 unknown2004
  D A B
  E A D
  F B E
  Z A B

It should be recoded as follows.

1 7 7 A unknown2000 unknown2000
2 7 8 B unknown2000 unknown2004
3 1 2 D A B
4 1 3 E A D
5 2 4 F B E
6 1 2 Z A B

Genotypes

Genotypes should be coded as 0/1/2 for {AA, Aa, aa} and 5 for missing as described elsewhere in this tutorial, in a text format with fixed file. The first column of this file contains (possibly alphanumeric) identifiers for animals, for instance:

   A 120120202102111
   Z 121111202111010

The only important requirement is the creation of the cross-reference file (usually called _XrefID). This file contains the original ID and the new ID in the renumbered pedigree and data files. In the previous example it would be:

 1  A
 6  Z

Overall mean

BLUPF90 programs do not include by default an overall mean !! If you need one, add it by yourself as a column of 1s in the data file