Question

How to convert a DnaStringSet object to list of seq?

0

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vinod.acear ▴ 50

@vinodacear-8884

Last seen 4.3 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 • 4.1k views

ADD COMMENT • link updated 7.5 years ago by Martin Morgan 25k • written 7.5 years ago by vinod.acear ▴ 50

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Haiying.Kong ▴ 110

@haiyingkong-9254

Last seen 5.7 years ago

Germany

Try:

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

ADD COMMENT • link 7.5 years ago Haiying.Kong ▴ 110

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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))?

ADD REPLY • link 7.5 years ago Martin Morgan 25k

score 2 · Accepted Answer · 2017-06-27

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 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?

ADD COMMENT • link 7.5 years ago Martin Morgan 25k

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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.

ADD REPLY • link 7.5 years ago vinod.acear ▴ 50