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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.

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    $\begingroup$ 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? $\endgroup$
    – Bioathlete
    Oct 14 '18 at 14:01
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Without giving away too much for your homework check out the sample() function in R. Think about how you can pass DNA bases to this function to generate random sequences.

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  • $\begingroup$ 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) $\endgroup$
    – EvaD
    Oct 13 '18 at 22:16
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    $\begingroup$ 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. $\endgroup$
    – gringer
    Oct 13 '18 at 23:47

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