brownsMethod

Merge p-values using the Brown's 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

brownsMethod 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></dl>

Arguments

Merge p-values using the Brown's method. — brownsMethod

<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>

</dl>

brownsMethod: Merge p-values using the Brown's method.

Description

Usage

Value

Arguments