FastKerFdr_signed

Provides functions for the joint analysis of Q sets of
p-values obtained for the same list of items. This joint analysis is
performed by querying a composite hypothesis, i.e. an arbitrary
complex combination of simple hypotheses, as described in Mary-Huard
et al. (2021) <doi:10.1093/bioinformatics/btab592> and De Walsche et
al.(2025) <doi: 10.1093/nargab/lqaf118>. In this approach, the Q-uplet
of p-values associated with each item is distributed as a multivariate
mixture, where each of the 2^Q components corresponds to a specific
combination of simple hypotheses. The dependence between the p-value
series is considered using a Gaussian copula function. A p-value for
the composite hypothesis test is derived from the posterior
probabilities.

Tristan Mary-Huard

Query Composite Hypotheses

Annaig De Walsche

Franck Gauthier

FastKerFdr_signed function

<dl><dt>X</dt>
<dd>a vector of probit-transformed p-values (corresponding to a p-value serie)</dd>
<dt>p0</dt>
<dd>a priori proportion of H0 hypotheses</dd>
<dt>plotting</dt>
<dd>boolean, should some diagnostic graphs be plotted. Default is FALSE.</dd>
<dt>NbKnot</dt>
<dd>The (maximum) number of knot for the kde procedure. Default is 1e5</dd>
<dt>tol</dt>
<dd>a tolerance value for convergence. Default is 1e-5</dd>
<dt>max_iter</dt>
<dd>the maximum number of iterations allowed for the algorithm to converge or complete its process.(Default is 1e4.)</dd></dl>

Arguments

FastKerFdr signed — FastKerFdr_signed

<dl>

<dt>X</dt>
<dd>a vector of probit-transformed p-values (corresponding to a p-value serie)</dd>


<dt>p0</dt>
<dd>a priori proportion of H0 hypotheses</dd>


<dt>plotting</dt>
<dd>boolean, should some diagnostic graphs be plotted. Default is FALSE.</dd>


<dt>NbKnot</dt>
<dd>The (maximum) number of knot for the kde procedure. Default is 1e5</dd>


<dt>tol</dt>
<dd>a tolerance value for convergence. Default is 1e-5</dd>


<dt>max_iter</dt>
<dd>the maximum number of iterations allowed for the algorithm to converge or complete its process.(Default is 1e4.)</dd>

</dl>

FastKerFdr_signed: FastKerFdr signed

Description

Usage

Value

Arguments