| Class | Analysis and data manipulation command |
| Name | skat |
| 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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