How to convert a DnaStringSet object to list of seq?
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vinod.acear ▴ 50
@vinodacear-8884
Last seen 4.2 years ago
India

Hi

Please help me to convert the DNA sequences of a "DNAStrinset" object to the list of DNA sequences.

Here is the description below:

Input:

> s1
  A DNAStringSet instance of length 5
    width seq
[1]     7 AGGCTCT
[2]     6 AGGTCT
[3]     7 AGGGTGT
[4]     7 AGGCTCT
[5]     7 TTCGGTA

 

I need following output in the form of list of sequences:

[[1]]
[1] "AGGCTCT"

[[2]]
[1] "AGGTCT"

[[3]]
[1] "AGGGTGT"

[[4]]
[1] "AGGCTCT"

[[5]]
[1] "TTCGGTA"

 

Thanks

dnastringset list stringset • 4.0k views
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2
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@martin-morgan-1513
Last seen 3 months ago
United States

as.list(as.character(s1)), but a very important question is why would you want to move from an efficient and compact representation to an inefficient one?

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0
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Thanks Martin.  I know  its inefficient way, but this was required as an input  for a already written function. I will try to modify it further.
 

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Haiying.Kong ▴ 110
@haiyingkong-9254
Last seen 5.6 years ago
Germany

Try:

lapply(1:length(s1), function(i) data.frame(s1)[i,1] )

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1
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FWIW, this is not very efficient R code, calling data.frame() for each element of DNAStringSet, and failing when s1 = DNAStringSet(). Can you make it more efficient (call data.frame(s1) only once) and robust (use seq_along(s1) instead of 1:length(s1))?

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