geneLists

This is a <code>list</code> object that contains the list background
genes and significant genes used in pathway enrichment. This object is
mostly meant for running examples and vignettes. The data provided is
for the rat, and is loaded from org.Rn.eg.db version 3.7.0.

datasets

Compare functional enrichment between two experimentally-derived groups of genes or proteins (Peterson, DR., et al.(2018)) <doi: 10.1371/journal.pone.0198139>. Given a list of gene symbols, 'diffEnrich' will
perform differential enrichment analysis using the Kyoto Encyclopedia of Genes
and Genomes (KEGG) REST API. This package provides a number of functions that are
intended to be used in a pipeline. Briefly, the user provides a KEGG formatted species id for either human, mouse or rat, and the package will
download and clean species specific ENTREZ gene IDs and map them to their respective
KEGG pathways by accessing KEGG's REST API. KEGG's API is used to guarantee the most up-to-date pathway data from KEGG. Next, the user will identify significantly
enriched pathways from two gene sets, and finally, the user will identify
pathways that are differentially enriched between the two gene sets. In addition to
the analysis pipeline, this package also provides a plotting function.

Harry Smith

diffEnrich

Given a List of Gene Symbols, Performs Differential Enrichment
Analysis

Laura Saba

geneLists function

A <code>list</code> with two names items which are:<dl class="dl-horizontal">
<dt>background</dt><dd>List of ENTREZ gene IDs that will considered background</dd>
<dt>sigGenes</dt><dd>List of ENTREZ gene IDs that were significant</dd>
</dl>

Format

geneLists — geneLists

A <code>list</code> with two names items which are:<dl class='dl-horizontal'>
<dt>background</dt><dd>List of ENTREZ gene IDs that will considered background</dd>
<dt>sigGenes</dt><dd>List of ENTREZ gene IDs that were significant</dd>
</dl>

geneLists: geneLists

Description

Usage

Arguments

Format