title: R memory.limit() command not able to handle vector allocation in genomic data
body: <p>I am dealing with large genomic data files. I try to process one with the following R code:</p>
  
  <pre><code>dj_annotatedhESC&lt;-annotate(djhESC, Nuc_hESC, "Nuc")
  </code></pre>
  
  <p><strong>Error: cannot allocate memory of size 5.8 Gb #debilitating error</strong></p>
  
  <p>The error highlighted in bold is due to the sheer size of the Nucleosome coverage vector. I tried to sort this problem out by using the command: "memory.limit(6000), memory.limit(8000) etc." and requesting different amounts of memory but this does not work.</p>
  
  <p>Although I came up with a temporary solution of reducing the size of the Nucleosome coverage file by taking the best ChIP-Seq reads- Is there a way that I can get around this (i.e. can I somehow request more memory for R, bearing in mind that I am using a <strong><em>linux cluster</em></strong> computer)?</p>