| Class | Analysis and data manipulation command |
| Name | pen |
| Arguments | <locus1> <locus2>) |
Performs Penrose [1935, 1937] sib-pair linkage statistics for two loci. Quantitative traits are treated as if categorical. The output consists of a two-by-two table of the sibling concordances at the two loci.
Example:
>> pen D13S162 D13S170
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Penrose Sib Pair Linkage Analysis for "D13S162" v. "D13S170"
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D13S170
D13S162 Concordant Discordant
Concordant 6 3
Discordant 3 36
No. of sib pairs = 48
No. of sibships = 13
No. complete observations = 48
LR contingency chi-square = 13.72
Degrees of freedom = 1
Asymptotic P-value = 0.0002
Cohen's Kappa = 0.5897
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