Merge p-values using the DPM method.

Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. Genes can be integrated using directional constraints that reflect how the input datasets are expected interact with one another. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The recent version of the package is part of the following publication: Directional integration and pathway enrichment analysis for multi-omics data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand J. Nature Communications (2024) <doi:10.1038/s41467-024-49986-4>.

Juri Reimand

ActivePathways

Integrative Pathway Enrichment Analysis of Multivariate Omics
Data

Jonathan Barenboim

Mykhaylo Slobodyanyuk

DPM function

<dl><dt>p_values</dt>
<dd>A matrix of m x n p-values.</dd>
<dt>data_matrix</dt>
<dd>An m x n matrix representing m tests and n samples. NA's are not allowed.</dd>
<dt>cov_matrix</dt>
<dd>A pre-calculated covariance matrix of <code>data_matrix</code>. This is more
efficient when making many calls with the same data_matrix.
Only one of <code>data_matrix</code> and <code>cov_matrix</code> must be given. If both are supplied,
<code>data_matrix</code> is ignored.</dd>
<dt>scores_direction</dt>
<dd>A matrix of log2 fold-change values. Datasets without directional information should be set to 0.</dd>
<dt>constraints_vector</dt>
<dd>A numerical vector of +1 or -1 values corresponding to the user-defined
directional relationship between columns in scores_direction. Datasets without directional information should
be set to 0.</dd></dl>

Arguments

Merge p-values using the DPM method. — DPM

<dl>

<dt>p_values</dt>
<dd>A matrix of m x n p-values.</dd>


<dt>data_matrix</dt>
<dd>An m x n matrix representing m tests and n samples. NA's are not allowed.</dd>


<dt>cov_matrix</dt>
<dd>A pre-calculated covariance matrix of <code>data_matrix</code>. This is more
efficient when making many calls with the same data_matrix.
Only one of <code>data_matrix</code> and <code>cov_matrix</code> must be given. If both are supplied,
<code>data_matrix</code> is ignored.</dd>


<dt>scores_direction</dt>
<dd>A matrix of log2 fold-change values. Datasets without directional information should be set to 0.</dd>


<dt>constraints_vector</dt>
<dd>A numerical vector of +1 or -1 values corresponding to the user-defined
directional relationship between columns in scores_direction. Datasets without directional information should
be set to 0.</dd>

</dl>

DPM: Merge p-values using the DPM method.

Description

Usage

Value

Arguments