Sib-pair Command: skat


ClassAnalysis and data manipulation command
Nameskat
Arguments <trait> [madsen_browning|beta_1_25_weights]

Performs SKAT combining all currently active markers. Analysis can be unweighted, or using two different allele frequency based weights.

Example:

>> include skat_example.in
[...]
Dataset used in examples from R SKAT package, which gives:

                SKAT p-values
    Linear   Weighted   +Covariates   Optimal
yc  0.862884 0.0187458  0.002877041   0.003849451
yb  0.949855 0.1145585  0.1401991     0.001588676

>> skat yc

--------------------------------------------------
 SKAT test for "yc"
 --------------------------------------------------
 Using unweighted linear kernel.

 Number of useful individuals = 2000
 Number of active markers     = 67 (mar1 -- mar67)
 Number of missing genotypes  = 0 (0.000)
 Trait mean                   = 0.2621 (SD=1.133)
 Skat test statistic          = 3119.
 Skat test P-value            = 0.8521

>> skat yc beta

--------------------------------------------------
 SKAT test for "yc"
 --------------------------------------------------
 Using SKAT default B(1,25) weighted linear kernel.

 Number of useful individuals = 2000
 Number of active markers     = 67 (mar1 -- mar67)
 Number of missing genotypes  = 0 (0.000)
 Trait mean                   = 0.2621 (SD=1.133)
 Skat test statistic          = 1557.
 Skat test P-value            = 0.0180

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