getURL

This function highlights the genes involved in the present GPS for a pathway
of interest in its diagram. Please note that this functionality is only
implemented for results of Reactome or KEGG based analyses.

functions

Pathway Analysis is statistically linking observations on
the molecular level to biological processes or pathways on
the systems(i.e., organism, organ, tissue, cell) level.
Traditionally, pathway analysis methods regard pathways
as collections of single genes and treat all genes in a pathway
as equally informative. However, this can lead to identifying
spurious pathways as statistically significant since components
are often shared amongst pathways. SIGORA seeks to avoid this
pitfall by focusing on genes or gene pairs that are (as a combination)
specific to a single pathway.
In relying on such pathway gene-pair signatures (Pathway-GPS),
SIGORA inherently uses the status of other genes in the
experimental context to identify the most relevant pathways.
The current version allows for pathway analysis of human
and mouse datasets. In addition, it contains pre-computed
Pathway-GPS data for pathways in the KEGG and  Reactome
pathway repositories and mechanisms for extracting GPS
for user-supplied repositories.

Witold Wolski

sigora

Signature Overrepresentation Analysis

Amir Foroushani

Fiona Brinkman

David Lynn

getURL function

<dl><dt>yy</dt>
<dd>A sigora analysis result object (created by <code>sigora</code>).</dd>
<dt>i</dt>
<dd>The rank position of the pathway of interest in summary_results.</dd></dl>

Arguments

Highlight the relevant genes for a specific pathway in its pathway diagram — getURL

<dl>

<dt>yy</dt>
<dd>A sigora analysis result object (created by <code>sigora</code>).</dd>


<dt>i</dt>
<dd>The rank position of the pathway of interest in summary_results.</dd>

</dl>

getURL: Highlight the relevant genes for a specific pathway in its pathway diagram

Description

Usage

Value

Arguments

See Also

Examples