Answers.Body: <p>Without giving away too much for your homework check out the <a href="http://www.rexamples.com/14/Sample()" rel="nofollow noreferrer"><code>sample()</code> function in R</a>. Think about how you can pass DNA bases to this function to generate random sequences. </p>
  
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Answers.CreationDate: 2018-10-13T22:16:26.330Z
Answers.Text: Thanks this is really helpful. Can you please help me understand the prob parameter, as I understand the probability of each element is relative to the entire list. Is it possible to specify probabilities for each element in certain positions? say I have `sample(1:2, size=4, replace=TRUE, prob=c(0.8, 0.2))` This says that 1 has probability 0.8 is the list overall, but I want to say 1 has probability 0.8 in position 4 (and some other probability in other positions)
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Answers.Text: This can't be done using just the `prob` parameter, because it only takes a single vector as input. You'll have to find some loopy, or otherwize crazy way *for* trying to *apply* different probabilities at different positions.
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Body: <p>Looking for some guidance.</p>
  
  <p>In an introductory bioinformatics class I am tasked with doing the following in R:</p>
  
  <ol>
  <li>Create the sequence ACTGACTG</li>
  <li>Generate a random string of nucleotides with equal probabilities.</li>
  </ol>
  
  <p>Are there certain functions that I should be looking at? No library or package or set of functions was provided so I am completely lost. I am assuming there must be functions in R that do these things that I need to manipulate, but I cannot seem to find any resources explaining that. I looked at seq() (thinking it might generate DNA sequences), but it only seems to generate sequences of integers. I also looked at randDNA(), but it is random, how could I make it generate the exact string in question 1).</p>
  
  <p>Any direction will be greatly appreciated.
  Thanks.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-14T14:01:23.200Z
Comments.Text: They are two separate problems.  If you have something that generates sequences of random integers can you think of a way to map those to the bases you want to report.  The first question is ambiguous.  How do your report the sequence you created?
Comments.UserDisplayName: Bioathlete
Tags: <genome-sequencing><homework>
Title: Generating basic dna sequences in R
ThreadText: # Generating basic dna sequences in R
  
  (Asked by: username_0 on 2018-10-13)
  
  Looking for some guidance.
  
  In an introductory bioinformatics class I am tasked with doing the following in R:
  
  1. Create the sequence ACTGACTG
  2. Generate a random string of nucleotides with equal probabilities.
  
  Are there certain functions that I should be looking at? No library or package or set of functions was provided so I am completely lost. I am assuming there must be functions in R that do these things that I need to manipulate, but I cannot seem to find any resources explaining that. I looked at seq() (thinking it might generate DNA sequences), but it only seems to generate sequences of integers. I also looked at randDNA(), but it is random, how could I make it generate the exact string in question 1).
  
  Any direction will be greatly appreciated.
  Thanks.
  
  **Tags:** genome-sequencing, homework
  
  > **Comments:**
  > **username_1**: They are two separate problems.  If you have something that generates sequences of random integers can you think of a way to map those to the bases you want to report.  The first question is ambiguous.  How do your report the sequence you created?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-10-13. Score: 1
  
  Without giving away too much for your homework check out the [`sample()` function in R](http://www.rexamples.com/14/Sample()). Think about how you can pass DNA bases to this function to generate random sequences.
  
  > **Comments:**
  > **username_0**: Thanks this is really helpful. Can you please help me understand the prob parameter, as I understand the probability of each element is relative to the entire list. Is it possible to specify probabilities for each element in certain positions? say I have `sample(1:2, size=4, replace=TRUE, prob=c(0.8, 0.2))` This says that 1 has probability 0.8 is the list overall, but I want to say 1 has probability 0.8 in position 4 (and some other probability in other positions)  
  > **username_3**: This can't be done using just the `prob` parameter, because it only takes a single vector as input. You'll have to find some loopy, or otherwize crazy way *for* trying to *apply* different probabilities at different positions.  
  
  ---
  
  