read.GMT

write.GMT

is.GMT

Functions to read and write Gene Matrix Transposed (GMT) files and to test if
an object inherits from GMT.

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

GMT function

A GMT object is a named list of terms, where each term is a list with the items:<dl>
 <dt>id</dt>
<dd>The term ID.</dd> <dt>name</dt>
<dd>The full name or description of the term.</dd> <dt>genes</dt>
<dd>A character vector of genes annotated to this term.</dd> 
</dl>

Format

<dl><dt>filename</dt>
<dd>Location of the gmt file.</dd>
<dt>gmt</dt>
<dd>A GMT object.</dd>
<dt>x</dt>
<dd>The object to test.</dd></dl>

Arguments

Read and Write GMT files — GMT

A GMT object is a named list of terms, where each term is a list with the items:<dl>
 <dt>id</dt>
<dd>The term ID.</dd>

 <dt>name</dt>
<dd>The full name or description of the term.</dd>

 <dt>genes</dt>
<dd>A character vector of genes annotated to this term.</dd>

 
</dl>

<dl>

<dt>filename</dt>
<dd>Location of the gmt file.</dd>


<dt>gmt</dt>
<dd>A GMT object.</dd>


<dt>x</dt>
<dd>The object to test.</dd>

</dl>

GMT: Read and Write GMT files

Description

Usage

Value

Format

Arguments

Details

Examples