title: convert table type from character/list to numeric (maSigPro, time series analysis, p.vector)
body: <p>I am totally new to R and I would like to perfom some time series analysis with the <code>maSigPro</code> package, based on different count tables.</p>
  
  <p>At the moment I am struggling with the data type for the <code>p.vector</code> function.
  The table with the TPM normalized counts are read in as follows:</p>
  
  <pre><code>counts_TPM =  as.matrix(read.table("TPM_Counts_25min.txt",  header=T, 
      row.names=1, stringsAsFactors=FALSE)
  counts_TPM=as.data.frame(counts_TPM, stringsAsFactors=FALSE)
  
  typeof(counts_TPM)
  # [1] "list"
  </code></pre>
  
  <p>This data type doesn't fit the p.vector function:</p>
  
  <pre><code>fit=p.vector(counts_TPM, sample_des_design, Q=0.05, counts=TRUE)
  # **Error** in FUN(newX[, i], ...) : invalid 'type' (character) of argument
  </code></pre>
  
  <p>This is a short outtake of my TPM normalized count table:</p>
  
  <pre><code>        E15R003a06  E15R003b06   E15R003c06  E15R003d13   E15R003d12  
  
      A    12.554467 12.68203563 1.436166e+01 13.58263382 1.312083e+01 
      B    10.392282 14.65197068 1.141320e+01  8.84738000 8.826718e+00 
      R    39.127930 42.10897757 4.194345e+01 34.76635026 3.005847e+01 
      X     6.696018  6.64936858 5.897263e+00  4.98501460 4.652471e+00  
      S    77.418782 84.95649902 8.017746e+01 82.99038040 7.884357e+01 
      T    53.565504 56.02217626 5.487839e+01 49.47038414 4.341778e+01 
  </code></pre>
  
  <p>I also tried <code>read.csv</code> with a csv format of my table and things like <code>data.matrix</code> (but this function is totally messing up my values), but I think I am missing one main point ....</p>
  
  <p>I hope someone can help me!</p>