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Marker Translation

You can define how markers are translated. Here is the default translation table

 -TranslationTable
     AA    2    2
     Aa    1    1
     aa    0    0
     A-   12   12
     a-   10   10
     --   -1   -1

Note a few things in the above translation table. There are six rows and three columns. There must be a token in all 18 positions of the table. The first column is the genotype. The program assumes that the $A$ allele is diagnostic for the High (parental 1) line and the $a$ allele is diagnostic for the Low (parental 2) line. A minus sign (-) means the allele is unkown. Dominant as well as codominant markers can be encoded. The middle column is how the output of these genotypes will be encoded while the right (3rd) column is how you will code the input of this file. The above TranslationTable maps 2 to 2, 1 to 1, 0 to 0, etc. Just about any set of tokens can be used for the third column, but DO NOT change the first two columns. If you encoded your $P_1$ homozygotes as $BB$, heterozygotes as $Bb$, etc, your translation table might appear as

 -TranslationTable
     AA    2   BB
     Aa    1   Bb
     aa    0   bb
     A-   12   B-
     a-   10   b-
     --   -1   --

Anything in the following data file that is not recognized (doesn't match something in column 3) will become unkown (-1) in the output.

REMEMBER: You need all 18 tokens following the -TranslationTable command and the first two columns can't be altered. You can only alter the last column.


next up previous contents index
Next: Crosses Up: Rcross input files Previous: Meanings of commands   Contents   Index
Christopher Basten 2002-03-27