orderedHypergeometric

Perform a series of hypergeometric tests (a.k.a. Fisher's Exact tests), on a ranked list of genes ordered
by significance against a list of annotation genes. The hypergeometric tests are executed with 
increasingly larger numbers of genes representing the top genes in order of decreasing scores. 
The lowest p-value of the series is returned as the optimal enriched intersection of the ranked list of genes
and the biological term (pathway).

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

orderedHypergeometric function

<dl><dt>genelist</dt>
<dd>Character vector of gene names, assumed to be ordered by decreasing importance. 
For example, the genes could be ranked by decreasing significance of differential expression.</dd>
<dt>background</dt>
<dd>Character vector of gene names. List of all genes used as a statistical background (i.e., the universe).</dd>
<dt>annotations</dt>
<dd>Character vector of gene names. A gene set representing a functional term, process or biological pathway.</dd></dl>

Arguments

Ordered Hypergeometric Test — orderedHypergeometric

<dl>

<dt>genelist</dt>
<dd>Character vector of gene names, assumed to be ordered by decreasing importance. 
For example, the genes could be ranked by decreasing significance of differential expression.</dd>


<dt>background</dt>
<dd>Character vector of gene names. List of all genes used as a statistical background (i.e., the universe).</dd>


<dt>annotations</dt>
<dd>Character vector of gene names. A gene set representing a functional term, process or biological pathway.</dd>

</dl>

orderedHypergeometric: Ordered Hypergeometric Test

Description

Usage

Value

Arguments

Examples