Subsetting a DNAStringSet object with many DNAString's
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dr ▴ 10
@dr-9473
Last seen 11 days ago
United States

Hi,

I have a Biostrings DNAStringSet object with many DNAStrings in it, and I want to subset each one of them from position 1 to the minimum between its length and a fixed cutoff.

So far I'm using a for loop for this, as in this example:

library(dplyr)
set.seed(1)
seq.set <- lapply(1:100, function(s) paste(sample(c("A","C","G","T"),as.integer(abs(rnorm(1,500,1000))),replace = T), collapse="")) %>%
  unlist() %>%
  Biostrings::DNAStringSet(.)

for(s in 1:length(seq.set))
  seq.set[s] <- Biostrings::subseq(seq.set[s], 1, min(650, Biostrings::width(seq.set[s])))

But because in reality the size of my DNAStringSet is ~200,000 DNAStrings it takes quite a while. Any faster solution?

Biostrings • 95 views
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Entering edit mode
dr ▴ 10
@dr-9473
Last seen 11 days ago
United States

Seems like an lapply to find the end point of each DNAStrings object in the DNAStringSet and then simply providing that as the end argument to the Biostrings::subseq function is the way to go:

library(dplyr)
set.seed(1)
seq.set <- lapply(1:100, function(s) paste(sample(c("A","C","G","T"),as.integer(abs(rnorm(1,500,1000))),replace = T), collapse="")) %>%
  unlist() %>%
  Biostrings::DNAStringSet(.)

seq.set.ends <- lapply(1:length(seq.set),function(i) min(650, Biostrings::width(seq.set[i]))) %>% unlist()
seq.set <- Biostrings::subseq(seq.set,start = rep(1,length(seq.set)),end = seq.set.ends)
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States

Try heads(x, cutoff)

H.

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