GHC_objective

Internal function to calculate the value of the kth GHC objective (possibly minus an offset)
when the kth p-value order statistic is x, for a set of size d.

internal

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

GHC_objective function

<dl><dt>x</dt>
<dd>The p-value of the kth p-value order statistic.</dd>
<dt>k</dt>
<dd>Which objective to use.</dd>
<dt>d</dt>
<dd>The size of the set.</dd>
<dt>offset</dt>
<dd>Used to zero the correct value when we put this into uniroot</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></dl>

Arguments

GHC_objective.R — GHC_objective

<dl>

<dt>x</dt>
<dd>The p-value of the kth p-value order statistic.</dd>


<dt>k</dt>
<dd>Which objective to use.</dd>


<dt>d</dt>
<dd>The size of the set.</dd>


<dt>offset</dt>
<dd>Used to zero the correct value when we put this into uniroot</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>

</dl>

GHC_objective: GHC_objective.R

Description

Usage

Value

Arguments

Examples