Class: SkatTest

stats~SkatTest()

Sequence kernel association test (SKAT).

See the original paper for details on the method, and our wiki for information on how the test is calculated using scores/covariances.

Constructor

new SkatTest()

Source:

Extends

  • AggregationTest

Methods

(static) weights(mafs, a, b)

Calculate typical SKAT weights using beta density function.

Parameters:
Name Type Default Description
mafs Array.<number>

Array of minor allele frequencies.
a number 1

alpha defaults to 1.
b number 25

beta defaults to 25.
Source:

run(u, v, w, mafs) → {Array.<Number>}

Calculate SKAT test.

The distribution function of the SKAT test statistic is evaluated using Davies' method by default. In the special case where there is only 1 lambda, the Liu moment matching approximation method is used.

Parameters:
Name Type Description
u Array.<Number>

Vector of score statistics (length m, number of variants).
v Array.<Number>

Covariance matrix of score statistics (m x m).
w Array.<Number>

Weight vector (length m, number of variants). If weights are not provided, they will be calculated using the default weights() method of this object.
mafs Array.<Number>

A vector of minor allele frequencies. These will be used to calculate weights if they were not provided.
Source:
Returns:

SKAT p-value.

Type
Array.<Number>