R.MLE

Gaussian copula correlation matrix Maximum Likelihood estimator.

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.(2023) <doi:10.1101/2024.03.17.585412>. 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

R.MLE function

<dl><dt>Hconfig</dt>
<dd>A list of all possible combination of \(H_0\) and \(H_1\) hypotheses generated by the <code>GetHconfig()</code> function.</dd>
<dt>zeta0</dt>
<dd>a matrix containing the \(\Phi(F_0(Z_{iq}))\), each column corresponding to a p-value serie.</dd>
<dt>zeta1</dt>
<dd>a matrix containing the \(\Phi(F_1(Z_{iq}))\), each column corresponding to a p-value serie.</dd>
<dt>Tau</dt>
<dd>a matrix providing for each item (in row) its posterior probability to belong to each of the H-configurations (in columns).</dd></dl>

Arguments

Gaussian copula correlation matrix Maximum Likelihood estimator. — R.MLE

<dl>

<dt>Hconfig</dt>
<dd>A list of all possible combination of \(H_0\) and \(H_1\) hypotheses generated by the <code>GetHconfig()</code> function.</dd>


<dt>zeta0</dt>
<dd>a matrix containing the \(\Phi(F_0(Z_{iq}))\), each column corresponding to a p-value serie.</dd>


<dt>zeta1</dt>
<dd>a matrix containing the \(\Phi(F_1(Z_{iq}))\), each column corresponding to a p-value serie.</dd>


<dt>Tau</dt>
<dd>a matrix providing for each item (in row) its posterior probability to belong to each of the H-configurations (in columns).</dd>

</dl>

R.MLE: Gaussian copula correlation matrix Maximum Likelihood estimator.

Description

Usage

Value

Arguments