breastcancer2012_subset

An example data set consisting of RNA-seq gene expression data, KEGG pathways, edge list and non-edge list.

datasets

Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.

Michael Hellstern

netgsa

Network-Based Gene Set Analysis

Ali Shojaie

Jing Ma

Kun Yue

breastcancer2012_subset function

A list with components<dl>
 <dt><code>x</code></dt>
<dd>The \(p \times n\) data matrix.</dd> <dt><code>group</code></dt>
<dd>The vector of class indicators of length \(n\).</dd> <dt><code>pathways</code></dt>
<dd>A list of KEGG pathways.</dd> <dt><code>edgelist</code></dt>
<dd>A data frame of edges, each row corresponding to one edge.</dd> <dt><code>nonedgelist</code></dt>
<dd>A data frame of nonedges, each row corresponding to one negative edge.</dd> <dt><code>pathways_mat</code></dt>
<dd>Matrix with pathway indicators</dd> 
</dl>

Format

Breast cancer data from TCGA (2012). This is a 750 gene subset — breastcancer2012_subset

A list with components<dl>
 <dt><code>x</code></dt>
<dd>The \(p \times n\) data matrix.</dd>

 <dt><code>group</code></dt>
<dd>The vector of class indicators of length \(n\).</dd>

 <dt><code>pathways</code></dt>
<dd>A list of KEGG pathways.</dd>

 <dt><code>edgelist</code></dt>
<dd>A data frame of edges, each row corresponding to one edge.</dd>

 <dt><code>nonedgelist</code></dt>
<dd>A data frame of nonedges, each row corresponding to one negative edge.</dd>

 <dt><code>pathways_mat</code></dt>
<dd>Matrix with pathway indicators</dd>

 
</dl>

breastcancer2012_subset: Breast cancer data from TCGA (2012). This is a 750 gene subset

Description

Usage

Arguments

Format

References

Examples