Calculate the difference of a known haplotype and the resulting unordered pair of snip pairs.

1 | ```
optimalfrequency(mm, mmorg)
``` |

`mm` |
This is a contigency table of two haplotype snips. 2x2 matrix or ndata.frame |

`mmorg` |
This is a contigency table of two diplotype snips pairs. |

The average squared distance to the expected result 3x3 table is used as a T statistic. The p value not to be zero is calculated. The higher the p value the more exact is the haplotype.

A list of values is returned.

`result\$LK` |
Linkage disequilibrium |

`result\$Testvalue` |
The squared sitance multiplied by the number of entries in 3x3 matrix mmorg |

`result\$prSimilarByChange` |
The probability not o be equal to zero by change. |

Jan wolfertz.

Stahel: Statistik fuer Naturwissenschaftler und Medizinier, pp. 107-120.

findoptimal

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