<!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>Load 10X count matrices from multiple directories — Read10X_Multi_Directory • scCustomize</title><!-- 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/flatly/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="Load 10X count matrices from multiple directories — Read10X_Multi_Directory"><meta property="og:description" content="Enables easy loading of sparse data matrices provided by 10X genomics that are present in multiple
subdirectories.  Can function with either default output directory structure of Cell Ranger or
custom directory structure."><!-- 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">scCustomize</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">2.1.2</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../index.html">Getting Started</a>
</li>
<li>
  <a href="../articles/Installation.html">Install</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    Vignettes
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu"><li class="dropdown-header">Plotting Vignettes</li>
    <li>
      <a href="../articles/Gene_Expression_Plotting.html">Plotting #1: General Analysis Plots</a>
    </li>
    <li>
      <a href="../articles/QC_Plots.html">Plotting #2: QC Plots</a>
    </li>
    <li>
      <a href="../articles/Sequencing_QC_Plots.html">Plotting #3: Sequencing QC Plots/Analysis</a>
    </li>
    <li>
      <a href="../articles/Iterative_Plotting.html">Plotting #4: Iterative Plotting Functions</a>
    </li>
    <li>
      <a href="../articles/Color_Palettes.html">Customized Color Palettes &amp; Themes</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Helpers &amp; Utilities</li>
    <li>
      <a href="../articles/Helpers_and_Utilities.html">General Helpers &amp; Utilities</a>
    </li>
    <li>
      <a href="../articles/Read_and_Write_Functions.html">Read &amp; Write Data Functions</a>
    </li>
    <li>
      <a href="../articles/Object_Conversion.html">Object/Assay Format Conversion</a>
    </li>
    <li>
      <a href="../articles/Markers_and_Cluster_Annotation.html">Marker Identification &amp; Cluster Annotation Helpers</a>
    </li>
    <li>
      <a href="../articles/Statistics.html">Statistics Functions</a>
    </li>
    <li>
      <a href="../articles/Update_Gene_Symbols.html">Updating Gene Symbols</a>
    </li>
    <li>
      <a href="../articles/Misc_Functions.html">Misc Functions</a>
    </li>
    <li class="divider">
    <li class="dropdown-header">Other Package Interactivity/Functions</li>
    <li>
      <a href="../articles/LIGER_Functions.html">LIGER Plotting &amp; Functionality</a>
    </li>
    <li>
      <a href="../articles/Cell_Bender_Functions.html">Cell Bender Functionality &amp; Plotting</a>
    </li>
  </ul></li>
<li>
  <a href="../news/index.html">News/Changelog</a>
</li>
<li>
  <a href="../reference/index.html">Reference</a>
</li>
<li>
  <a href="../articles/FAQ.html">FAQ</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://github.com/samuel-marsh/scCustomize/" class="external-link">
    <span class="fab fa-github fa-lg"></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>Load 10X count matrices from multiple directories</h1>
    <small class="dont-index">Source: <a href="https://github.com/samuel-marsh/scCustomize/blob/HEAD/R/Read_&amp;_Write_Data.R" class="external-link"><code>R/Read_&amp;_Write_Data.R</code></a></small>
    <div class="hidden name"><code>Read10X_Multi_Directory.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Enables easy loading of sparse data matrices provided by 10X genomics that are present in multiple
subdirectories.  Can function with either default output directory structure of Cell Ranger or
custom directory structure.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">Read10X_Multi_Directory</span><span class="op">(</span></span>
<span>  <span class="va">base_path</span>,</span>
<span>  secondary_path <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  default_10X_path <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  cellranger_multi <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  sample_list <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  sample_names <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  parallel <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  num_cores <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  merge <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  <span class="va">...</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>base_path</dt>
<dd><p>path to the parent directory which contains all of the subdirectories of interest.</p></dd>


<dt>secondary_path</dt>
<dd><p>path from the parent directory to count matrix files for each sample.</p></dd>


<dt>default_10X_path</dt>
<dd><p>logical (default TRUE) sets the secondary path variable to the default 10X
directory structure.</p></dd>


<dt>cellranger_multi</dt>
<dd><p>logical, whether samples were processed with Cell Ranger <code>multi</code>, default is FALSE.</p></dd>


<dt>sample_list</dt>
<dd><p>a vector of sample directory names if only specific samples are desired.  If <code>NULL</code> will
read in subdirectories in parent directory.</p></dd>


<dt>sample_names</dt>
<dd><p>a set of sample names to use for each sample entry in returned list.  If <code>NULL</code> will
set names to the subdirectory name of each sample.</p></dd>


<dt>parallel</dt>
<dd><p>logical (default FALSE) whether or not to use multi core processing to read in matrices.</p></dd>


<dt>num_cores</dt>
<dd><p>how many cores to use for parallel processing.</p></dd>


<dt>merge</dt>
<dd><p>logical (default FALSE) whether or not to merge samples into a single matrix or return
list of matrices.  If TRUE each sample entry in list will have cell barcode prefix added.  The prefix
will be taken from <code>sample_names</code>.</p></dd>


<dt>...</dt>
<dd><p>Extra parameters passed to <code><a href="https://satijalab.org/seurat/reference/Read10X.html" class="external-link">Read10X</a></code>.</p></dd>

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

<p>a list of sparse matrices (merge = FALSE) or a single sparse matrix (merge = TRUE).</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="va">base_path</span> <span class="op">&lt;-</span> <span class="st">'path/to/data/directory'</span></span></span>
<span class="r-in"><span><span class="va">expression_matrices</span> <span class="op">&lt;-</span> <span class="fu">Read10X_Multi_Directory</span><span class="op">(</span>base_path <span class="op">=</span> <span class="va">base_path</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-in"><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 Samuel Marsh.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer></div>

  


  

  </body></html>

