title: how to create a table as dunn.test output (R)?
body: <p>I'm working with bacteria pyrosequencing data and I'm doing the statistical analysis with R. I have 21 samples and 7 different treatments. I loaded my data into R phyloseq obtaining:</p>
  
  <pre><code>&gt; psR
  phyloseq-class experiment-level object
  otu_table()   OTU Table:         [ 7498 taxa and 21 samples ]
  sample_data() Sample Data:       [ 21 samples by 8 sample variables ]
  tax_table()   Taxonomy Table:    [ 7498 taxa by 6 taxonomic ranks ]
  phy_tree()    Phylogenetic Tree: [ 7498 tips and 7497 internal nodes ]
  </code></pre>
  
  <p>Since I found that there are statistically significant differences between the treaments (with the adonis function), I wanted to know which OTUs have a different abundance in the different treatments. To do that I used the function dunn.test (with Kruskal-Wallis test incorporated), swapping first the rows and the columns in the OTU table in order to apply the test:</p>
  
  <pre><code>swap_otu_table &lt;- t(otu_table(psR))
  treatment &lt;- c('A', 'A', 'A', 'B', 'B', 'B', 'C', 'C', 'C', 'D', 'D', 'D', 'E', 'E', 'E', 'F', 'F', 'F', 'G', 'G', 'G')
  swap_otu_tableDF &lt;- as.data.frame(swap_otu_table)
  ncol(swap_otu_tableDF)
  [1] 7498
  lapply(swap_otu_tableDF[1:7498], function(x) kruskal.test(x ~ treatment,   data=swap_otu_tableDF))
  </code></pre>
  
  <p>The output of this recursive function is quite difficult to read, especially for all 7498 OTUs. </p>
  
  <p>Is there some way to apply a Kruskal-Wallis + Dunn's test in a recursive way that gives a table as an output, preferably in order of significance, and with not only the OTU code but also the taxonomic identification contained in tax_table(psR)?</p>
  
  <p>Thank you very much!</p>
  
  <p>Lidia</p>