title: write.table R failing
body: <p>I'm running a small script, it works ok, but whenever I try to write the dataframe, the number of rows that I get as output (32933) is different from the number of rows that I'm expecting (18285).</p>
  
  <pre><code>datsort &lt;- read.table("/home/.../vep_data_sorted.csv", header = T, sep="\t", fill = T)
  dim(datsort)
  #[1] 97059    47
  
  datsort &lt;- datsort[which(datsort$variation_type == "SNV"),]
  dim(datsort)
  #[1] 40954    47
  
  gmaf &lt;- as.numeric(as.character(datsort$GMAF_freq))
  exac &lt;- as.numeric(as.character(datsort$ExAC))
  
  gmaf[which(is.na(gmaf) == T)] &lt;- 0
  exac[which(is.na(exac) == T)] &lt;- 0
  
  x &lt;- which(gmaf &lt; 1)
  y &lt;- which(exac &lt; 1)
  
  int &lt;- intersect(x,y)
  length(int)
  #[1] 18285
  
  datsort &lt;- datsort[int,]
  dim(datsort)
  #[1] 18285    47
  
  write.table(datsort, "/home/.../vep_data_sorted_1per.csv", sep="\t", quote = F, row.names = F)
  </code></pre>
  
  <p>Then I check the the number of lines and columns</p>
  
  <pre><code>#Rows    
  wc -l vep_data_sorted_1per.csv
  32933 vep_data_sorted_1per.csv
  #Column
  awk -F '\t' '{print NF}' vep_data_sorted_1per.csv | sort -nu | tail -n 1
  47
  </code></pre>
  
  <p>Any suggestion of what I'm missing?
  Thanks</p>