Question

Recycling a DNAStringSet over an IRangesList in extractAt()

0

Entering edit mode

Nicholas Cooley • 0

@Nicholas-24385

Last seen 24 months ago

United States

I've gotten myself into a situation where I'd like to use extractAt to pull multiple IRangesList positions from a DNAStringSet. A very simple version of what I'm trying to do would start with:

seqs <- DNAStringSet("ATCGTA")
v01 <- IRangesList(IRanges(start = c(1, 4),
                           end = c(3, 6)),
                   IRanges(start = c(1, 3, 5),
                           end = c(2, 4, 6)))

However this will error out complaining that the lengths are not matched.

v02 <- extractAt(x = seqs, at = v01)

Is there a simple way to perform this kind of operation, returning a DNAStringSetList is likely the goal in the short term.

Biostrings IRanges • 1.0k views

ADD COMMENT • link 3.4 years ago Nicholas Cooley • 0

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You could use either of these two options:

#/ either:
v02 <- extractAt(x = seqs, at = do.call(c, v01))

#/ or:
v02 <- lapply(v01, function(z) extractAt(x = seqs, at = z))

ADD REPLY • link 3.4 years ago ATpoint ★ 4.0k

score 2 · Accepted Answer · 2020-12-15

2

Entering edit mode

Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

extractAt() could gain support for recycling x. In the mean time, you can just do:

extractAt(rep(seqs, length=length(v01)), v01)

ADD COMMENT • link 3.4 years ago Michael Lawrence ★ 11k

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This will work great in the short term! Recycling would I think be preferable, especially in cases where seqs is very large. Thanks!

ADD REPLY • link 3.4 years ago Nicholas Cooley • 0