optimalfrequency {AlgebraicHaploPackage}

Evaluate potential haplotypes.

Description

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.

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.

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.

Author(s)

Jan wolfertz.

References

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

See Also

findoptimal