f1_separation_signed

Signed case function: Separate f1 into f+ and f-

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

f1_separation_signed function

<dl><dt>XMat</dt>
<dd>a matrix of probit-transformed p-values, each column corresponding to a p-value serie.</dd>
<dt>f0Mat</dt>
<dd>a matrix containing the evaluation of the marginal density functions under \(H_0\) at each items,
each column corresponding to a p-value serie.</dd>
<dt>f1Mat</dt>
<dd>a matrix containing the evaluation of the marginal density functions under \(H_1\) at each items,
each column corresponding to a p-value serie.</dd>
<dt>p0</dt>
<dd>the proportions of \(H_0\) items for each series.</dd>
<dt>plotting</dt>
<dd>boolean, should some diagnostic graphs be plotted. (Default is FALSE.)</dd></dl>

Arguments

Signed case function: Separate f1 into f+ and f- — f1_separation_signed

<dl>

<dt>XMat</dt>
<dd>a matrix of probit-transformed p-values, each column corresponding to a p-value serie.</dd>


<dt>f0Mat</dt>
<dd>a matrix containing the evaluation of the marginal density functions under \(H_0\) at each items,
each column corresponding to a p-value serie.</dd>


<dt>f1Mat</dt>
<dd>a matrix containing the evaluation of the marginal density functions under \(H_1\) at each items,
each column corresponding to a p-value serie.</dd>


<dt>p0</dt>
<dd>the proportions of \(H_0\) items for each series.</dd>


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

</dl>

`f1plusMat`	a matrix containing the evaluation of the marginal density functions under \(H_1^+\) at each items, each column corresponding to a p-value serie.
`f1minusMat`	a matrix containing the evaluation of the marginal density functions under \(H_1^-\) at each items, each column corresponding to a p-value serie.
`p1plus`	an estimate of the proportions of \(H_1^+\) items for each series.
`p1minus`	an estimate of the proportions of \(H_1^-\) items for each series.

f1_separation_signed: Signed case function: Separate f1 into f+ and f-

Description

Usage

Value

Arguments