GBJ_pvalue

Calculate the p-value for the Generalized Berk-Jones (GBJ) statistic.

Offers the Generalized Berk-Jones (GBJ) test for set-based inference in genetic
association studies. The GBJ is designed as an alternative to tests such as Berk-Jones (BJ),
Higher Criticism (HC), Generalized Higher Criticism (GHC), Minimum p-value (minP), and Sequence
Kernel Association Test (SKAT). All of these other methods (except for SKAT) are also implemented
in this package, and we additionally provide an omnibus test (OMNI) which integrates information from each of the tests.
The GBJ has been shown to outperform other tests in genetic association studies when signals
are correlated and moderately sparse. Please see the vignette for a quickstart guide or Sun and Lin
(2017) <arXiv:1710.02469> for more details.

Ryan Sun

Generalized Berk-Jones Test for Set-Based Inference in Genetic
Association Studies

GBJ_pvalue function

<dl><dt>observed_gbj</dt>
<dd>The observed value of the GBJ statistic.</dd>
<dt>d</dt>
<dd>The number of test statistics in the set.</dd>
<dt>pairwise_cors</dt>
<dd>A vector of all d(d-1)/2 pairwise correlations between the test
statistics, where d is total number of test statistics in the set.</dd>
<dt>times_to_try</dt>
<dd>Sometimes the numerical root-finder is finnicky, so we have to give
it extra chances to try and calculate the p-value if first time is failure. Recommend
setting this parameter to 5.</dd></dl>

Arguments

GBJ_pvalue.R — GBJ_pvalue

<dl>

<dt>observed_gbj</dt>
<dd>The observed value of the GBJ statistic.</dd>


<dt>d</dt>
<dd>The number of test statistics in the set.</dd>


<dt>pairwise_cors</dt>
<dd>A vector of all d(d-1)/2 pairwise correlations between the test
statistics, where d is total number of test statistics in the set.</dd>


<dt>times_to_try</dt>
<dd>Sometimes the numerical root-finder is finnicky, so we have to give
it extra chances to try and calculate the p-value if first time is failure. Recommend
setting this parameter to 5.</dd>

</dl>

GBJ_pvalue: GBJ_pvalue.R

Description

Usage

Value

Arguments

Examples