Answers.Body: <p><em>Answer from @fabio-marroni, converted from comment:</em></p>
  <p>You might try to use <a href="https://bioconductor.org/packages/release/bioc/vignettes/MutationalPatterns/inst/doc/Introduction_to_MutationalPatterns.pdf" rel="nofollow noreferrer">mutationalPatterns</a> and see if the  responders cluster together and separated from nonresponders.</p>
  
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Answers.CreationDate: 2021-07-14T11:32:17.673Z
Answers.LastActivityDate: 2021-07-14T11:32:17.673Z
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Body: <p>I have mutational catalogues of 4 samples like below</p>
  <pre><code>&gt; head(out)
          Responders1 Nonresponders1 Responders2 Nonresponders2
  A[C&gt;A]A       11744          13546        2897           3655
  A[C&gt;A]C        5144           7172        2295           2163
  A[C&gt;A]G         939           1257         290            279
  A[C&gt;A]T        6065           7997        2078           2088
  C[C&gt;A]A        8969          11155        2055           2582
  C[C&gt;A]C        4050           6657        1367           1173
  &gt;
  
   &gt; dim(mut)
  [1] 96  4
  &gt; 
  </code></pre>
  <p><em>Note: A[C&gt;A]A - Single nucleotide base substitution</em></p>
  <p>I want to look if mutational substitutions are different between samples</p>
  <p>I have tried</p>
  <pre><code>wilcox.test(mut<span class="math-container">$Responders2,mut$</span>Nonresponders2)
  
  t.test(mut<span class="math-container">$Responders2,mut$</span>Nonresponders2)
  
  var.test(mut<span class="math-container">$Responders2,mut$</span>Nonresponders2)
  fisher.test(mut<span class="math-container">$Responders2,mut$</span>Nonresponders2,simulate.p.value=TRUE)
  
  kruskal.test(mut<span class="math-container">$Responders2,mut$</span>Nonresponders2)
  </code></pre>
  <p>To find a difference but I think you may know a better test to find any difference here</p>
  <p>This is base shift (mutation, substitution across genome of each patient). I guess mutations happen randomly but I don't know if mutational caller algorithm also pick them by randomness. I expect the shift of A (Adenine) to C (Cytosine) in a group of these patients be higher than the other group. This higher rate likely should be due to some background than randomness picked by algorithm. So I think null hypothesis is that rate of base shifting is not the same in both group. I also don't expect a normalised distribution of base shifting rather a poison distribution.</p>
  <p>Can you help please?</p>
  <p>Thanks</p>
  
Tags: <r><wgs><mutations>
Title: Finding difference between groups
ThreadText: # Finding difference between groups
  
  (Asked by: username_0 on 2020-03-21)
  
  I have mutational catalogues of 4 samples like below
  
  ```
  > head(out)
          Responders1 Nonresponders1 Responders2 Nonresponders2
  A[C>A]A       11744          13546        2897           3655
  A[C>A]C        5144           7172        2295           2163
  A[C>A]G         939           1257         290            279
  A[C>A]T        6065           7997        2078           2088
  C[C>A]A        8969          11155        2055           2582
  C[C>A]C        4050           6657        1367           1173
  >
  
   > dim(mut)
  [1] 96  4
  > 
  
  ```
  
  *Note: A[C>A]A - Single nucleotide base substitution*
  
  I want to look if mutational substitutions are different between samples
  
  I have tried
  
  ```
  wilcox.test(mut$Responders2,mut$Nonresponders2)
  
  t.test(mut$Responders2,mut$Nonresponders2)
  
  var.test(mut$Responders2,mut$Nonresponders2)
  fisher.test(mut$Responders2,mut$Nonresponders2,simulate.p.value=TRUE)
  
  kruskal.test(mut$Responders2,mut$Nonresponders2)
  
  ```
  
  To find a difference but I think you may know a better test to find any difference here
  
  This is base shift (mutation, substitution across genome of each patient). I guess mutations happen randomly but I don't know if mutational caller algorithm also pick them by randomness. I expect the shift of A (Adenine) to C (Cytosine) in a group of these patients be higher than the other group. This higher rate likely should be due to some background than randomness picked by algorithm. So I think null hypothesis is that rate of base shifting is not the same in both group. I also don't expect a normalised distribution of base shifting rather a poison distribution.
  
  Can you help please?
  
  Thanks
  
  **Tags:** r, wgs, mutations
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-07-14. Score: 1
  
  *Answer from @fabio-marroni, converted from comment:*
  
  You might try to use [mutationalPatterns](https://bioconductor.org/packages/release/bioc/vignettes/MutationalPatterns/inst/doc/Introduction_to_MutationalPatterns.pdf) and see if the responders cluster together and separated from nonresponders.
  
  
  ---
  
  