<!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>Platypus V2 Differentially expressed genes — GEX_DEgenes_persample • Platypus</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/yeti/bootstrap.min.css" rel="stylesheet" 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="Platypus V2 Differentially expressed genes — GEX_DEgenes_persample"><meta property="og:description" content='!Only for Platypus version v2. For more flexibility and platypus v3 please refer to GEX_Degenes. Extracts the differentially expressed genes between two samples. This function uses the FindMarkers function from the Seurat package. Further parameter control can be accomplished by calling the function directly on the output of automate_GEX and further extracting sample information from the "sample_id" component of the Seurat object.'><!-- 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">Platypus</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">3.4.1</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../index.html">
    <span class="fa fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../articles/quickstart.html">Get started</a>
</li>
<li>
  <a href="../vignette_index.html">Vignettes</a>
</li>
<li>
  <a href="../PlatypusDB_index.html">PlatypusDB</a>
</li>
<li>
  <a href="../reference/index.html">Functions</a>
</li>
<li>
  <a href="../news/index.html">News</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    Other Packages
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu"><li>
      <a href="https://immunesim.readthedocs.io/en/latest/" class="external-link">ImmuneSIM</a>
    </li>
  </ul></li>
<li>
  <a href="../cute_monotremes.html">Cute Monotremes</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://twitter.com/alexyermanos" class="external-link">
    <span class="fa fa-twitter"></span>
     
  </a>
</li>
<li>
  <a href="https://twitter.com/KreineVic" class="external-link">
    <span class="fa fa-twitter"></span>
     
  </a>
</li>
<li>
  <a href="https://github.com/alexyermanos/Platypus" class="external-link">
    <span class="fa fa-github"></span>
     
  </a>
</li>
      </ul></div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Platypus V2 Differentially expressed genes</h1>
    <small class="dont-index">Source: <a href="https://github.com/alexyermanos/Platypus/tree/masterR/GEX_DEgenes_persample.R" class="external-link"><code>R/GEX_DEgenes_persample.R</code></a></small>
    <div class="hidden name"><code>GEX_DEgenes_persample.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>!Only for Platypus version v2. For more flexibility and platypus v3 please refer to GEX_Degenes. Extracts the differentially expressed genes between two samples. This function uses the FindMarkers function from the Seurat package. Further parameter control can be accomplished by calling the function directly on the output of automate_GEX and further extracting sample information from the "sample_id" component of the Seurat object.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">GEX_DEgenes_persample</span><span class="op">(</span></span>
<span>  <span class="va">automate.GEX</span>,</span>
<span>  <span class="va">min.pct</span>,</span>
<span>  <span class="va">sample1</span>,</span>
<span>  <span class="va">sample2</span>,</span>
<span>  <span class="va">by.group</span>,</span>
<span>  <span class="va">filter</span>,</span>
<span>  <span class="va">return.plot</span>,</span>
<span>  <span class="va">logFC</span>,</span>
<span>  <span class="va">up.genes</span>,</span>
<span>  <span class="va">down.genes</span>,</span>
<span>  <span class="va">base</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>automate.GEX</dt>
<dd><p>Output Seurat object from automate_GEX function that contained at least two distinct biological samples. The differential biological samples correspond to integer values in the order of the working directories initially supplied to the automate_GEX function.</p></dd>


<dt>min.pct</dt>
<dd><p>The minimum percentage of cells expressing a gene in either of the two groups to be compared.</p></dd>


<dt>sample1</dt>
<dd><p>either character or integer specifying the first sample that should be compared.</p></dd>


<dt>sample2</dt>
<dd><p>either character or integer specifying the first sample that should be compared.</p></dd>


<dt>by.group</dt>
<dd><p>Logical specifying if groups should be used instead of samples. If TRUE, then the argument in sample1 and sample2 will correspond to cells found in the groups from sample1 or sample2.</p></dd>


<dt>filter</dt>
<dd><p>Character vector of initials of the genes to be filtered. Default is c("MT-", "RPL", "RPS"), which filters mitochondrial and ribosomal genes.</p></dd>


<dt>return.plot</dt>
<dd><p>Logical specifying if a heatmap of the DEX genes is to be returned. If TRUE then @return is a list where the first element is a dataframe and the second a heatmap (see @return)</p></dd>


<dt>logFC</dt>
<dd><p>Logical specifying whether the genes will be displayed based on logFC (TRUE) or pvalue (FALSE).</p></dd>


<dt>up.genes</dt>
<dd><p>Integer specifying the number of upregulated genes to be shown.</p></dd>


<dt>down.genes</dt>
<dd><p>Integer specifying the number of downregulated genes to be shown.</p></dd>


<dt>base</dt>
<dd><p>The base with respect to which logarithms are computed. Default: 2</p></dd>

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

<p>Returns a dataframe containing the output from the FindMarkers function, which contains information regarding the genes that are differentially regulated, statistics (p value and log fold change), and the percent of cells expressing the particular gene for both groups.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span><span class="fu">GEX_DEgenes_persample</span><span class="op">(</span>automate.GEX<span class="op">=</span><span class="va">automate.GEX.output</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span></span></span>
<span class="r-in"><span>,min.pct <span class="op">=</span> <span class="fl">.25</span>,sample1 <span class="op">=</span> <span class="st">"1"</span>,sample2 <span class="op">=</span> <span class="st">"2"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></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 Alexander Yermanos.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
</div>

      </footer></div>

  


  

  </body></html>

