<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Search Pathways in GO/Reactome Database — SearchDatabase • SeuratExtend</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Search Pathways in GO/Reactome Database — SearchDatabase"><meta property="og:description" content="Search for pathways in the GO or Reactome database using a gene name, pathway ID (SetID), or pathway name (SetName)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
    

    <div class="container template-reference-topic">
      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">SeuratExtend</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.0.0</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../reference/index.html">Reference</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Search Pathways in GO/Reactome Database</h1>
    
    <div class="hidden name"><code>SearchDatabase.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Search for pathways in the GO or Reactome database using a gene name, pathway ID (SetID), or pathway name (SetName).</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SearchDatabase</span><span class="op">(</span></span>
<span>  <span class="va">item</span>,</span>
<span>  type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"gene"</span>, <span class="st">"SetID"</span>, <span class="st">"SetName"</span><span class="op">)</span>,</span>
<span>  database <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"GO"</span>, <span class="st">"Reactome"</span><span class="op">)</span>,</span>
<span>  spe <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"spe"</span><span class="op">)</span>,</span>
<span>  export.to.data.frame <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  n.min <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  n.max <span class="op">=</span> <span class="cn">Inf</span>,</span>
<span>  only.end.terms <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  return <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"all"</span>, <span class="st">"ID"</span>, <span class="st">"genelist"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>item</dt>
<dd><p>A gene name, pathway ID, or pathway name.</p></dd>


<dt>type</dt>
<dd><p>Types of search criteria. Can be one or a combination of "gene", "SetID", "SetName". Default: c("gene", "SetID", "SetName").</p></dd>


<dt>database</dt>
<dd><p>The database to search in: "GO", "Reactome", or both. Default: c("GO", "Reactome").</p></dd>


<dt>spe</dt>
<dd><p>Species, either 'human' or 'mouse'. Default: getOption("spe").</p></dd>


<dt>export.to.data.frame</dt>
<dd><p>If TRUE, the results will be returned as a data frame, which can be easily exported to csv or xlsx formats. Default: FALSE.</p></dd>


<dt>n.min</dt>
<dd><p>Minimum number of genes required in the gene set. Default: 1.</p></dd>


<dt>n.max</dt>
<dd><p>Maximum number of genes allowed in the gene set. Default: Inf.</p></dd>


<dt>only.end.terms</dt>
<dd><p>If TRUE, only the end-level pathways or gene sets will be returned. Default: FALSE.</p></dd>


<dt>return</dt>
<dd><p>Specifies the format of the result. If set to "all" (default), the result will include all information (pathway ID, pathway name, genes). If set to "ID", it will only return a vector of pathway IDs. If set to "genelist", it will return a list where the names are pathway IDs and the contents are the corresponding genes.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>Depending on the specified parameters, the function returns:</p><ul><li><p>A full list (with pathway ID, pathway name, and genes) if <code>return = "all"</code>.</p></li>
<li><p>A vector of pathway IDs if <code>return = "ID"</code>.</p></li>
<li><p>A named list of genes with pathway IDs as the list names if <code>return = "genelist"</code>.</p></li>
<li><p>A data frame if <code>export.to.data.frame = TRUE</code>.</p></li>
</ul></div>
    <div id="details">
    <h2>Details</h2>
    <p>Further details and usage can be seen in the provided examples.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">SeuratExtend</span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>max.print <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Set the default database search to 'human'</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>spe <span class="op">=</span> <span class="st">"human"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># The 'item' parameter can be anything like a gene, pathway ID, or pathway name.</span></span>
<span><span class="co"># For example, search in the GO/Reactome database for pathways that contain the "CD3D" gene</span></span>
<span><span class="co"># or pathway names that include "metabolic".</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CD3D"</span>,<span class="st">"metabolic"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">result</span>, <span class="fl">5</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># If you only want to search based on gene names, you can specify this in the 'type' parameter.</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="st">"CD3D"</span>, type <span class="op">=</span> <span class="st">"gene"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># If you want to search in a specific database, you can specify it using the 'database' parameter.</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="st">"CD3D"</span>, database <span class="op">=</span> <span class="st">"Reactome"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># You can specify the database to be either 'human' or 'mouse' using the 'spe' parameter.</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="st">"Cd3d"</span>, spe <span class="op">=</span> <span class="st">"mouse"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">result</span>, <span class="fl">5</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># If you only want the result to be a list of pathway IDs, which could be useful for subsequent analysis,</span></span>
<span><span class="co"># you can set the 'return' parameter accordingly.</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="st">"CD3D"</span>, return <span class="op">=</span> <span class="st">"ID"</span><span class="op">)</span></span>
<span><span class="va">result</span></span>
<span></span>
<span><span class="co"># If you want the output as a gene list, with the IDs as names, suitable for inputs like GeneSetAnalysis,</span></span>
<span><span class="co"># you can adjust the 'return' parameter.</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="st">"CD3D"</span>, return <span class="op">=</span> <span class="st">"genelist"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">result</span>, <span class="fl">5</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># If you prefer the output to be a data frame, which is suitable for exporting to Excel or CSV formats,</span></span>
<span><span class="co"># you can set 'export.to.data.frame' to TRUE.</span></span>
<span><span class="va">result</span> <span class="op">&lt;-</span> <span class="fu">SearchDatabase</span><span class="op">(</span><span class="st">"CD3D"</span>, export.to.data.frame <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">result</span><span class="op">)</span></span></code></pre></div>
    </div>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
    </nav></div>
</div>


      <footer><div class="copyright">
  <p></p><p>Developed by Yichao Hua.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
</div>

      </footer></div>

  


  

  </body></html>

