Calculate the difference of a known haplotype and the resulting unordered pair of snip pairs.
Usage
optimalfrequency(mm, mmorg)
Arguments
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.
Value
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.
Details
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.
References
Stahel: Statistik fuer Naturwissenschaftler und Medizinier, pp. 107-120.