Sib-pair Command: pen

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
---------------------------------------------------------------
Penrose Sib Pair Linkage Analysis for "D13S162" v. "D13S170"
---------------------------------------------------------------

                     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