Extend range in both directions

Question

I have a GRanges object and I would like to extend all ranges eg 1kb on both sides, so each range will become 2kb longer. It is strange but I couldn't manage to do this using the inter-range-methods of GenomicRanges or IRanges. One way that would produce the desired result is to use resize twice, to first extend the 5' and then the 3'. But this of course is extremely awkward. Isn't there a more direct way of doing this? Please advice

gr <- GRanges(c('chr1','chr1'), IRanges(start=c(20, 120), width=10), strand='+')
gr <- resize(gr, fix='start', width=width(gr)+10)
gr <- resize(gr, fix='end', width=width(gr)+10)
gr

score 9 · Accepted Answer · answered Jan 12 '17 at 21:16

9

GRanges supports operators such as - and +

gr + 10

will do the trick.

answered Jan 12 '17 at 21:16

crazyhottommy

310
1
3
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score 5 · Answer 2 · answered Dec 17 '15 at 11:14

It's very simple. You can use start and end functions in GenomicRanges.

gr <- GRanges(c('chr1','chr1'), IRanges(start=c(20, 120), width=10), strand='+')
gr
# GRanges object with 2 ranges and 0 metadata columns:
#       seqnames     ranges strand
#          <Rle>  <IRanges>  <Rle>
#   [1]     chr1 [ 20,  29]      +
#   [2]     chr1 [120, 129]      +
#   -------
#   seqinfo: 1 sequence from an unspecified genome; no seqlengths

start(gr) <- start(gr) - 10
end(gr) <- end(gr) + 10
gr
# GRanges object with 2 ranges and 0 metadata columns:
#      seqnames     ranges strand
#         <Rle>  <IRanges>  <Rle>
#  [1]     chr1 [ 10,  39]      +
#  [2]     chr1 [110, 139]      +
#  -------
#  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Sure. But since there are so many functions for changing ranges (resize, narrow, etc), or defining new ranges based on existing (flanks, promoters) I expected a dedicated function capable of doing this fairly simple but (I think) very useful operation. — Ludo, Dec 17 '15 at 15:01

score 3 · Answer 3 · answered Feb 28 '20 at 15:33

3

Three years later but...

A direct way of do that is using resize method of GRanges with fix parameter:

gr <- resize(gr, width = width(gr)+(desired_size*2), fix = "center")

answered Feb 28 '20 at 15:33

Sergio Lois

51
2

score -1 · Answer 4 · answered Aug 03 '21 at 14:21

-1

You can use flank:

gr <- flank(gr, width=10, both=TRUE)

answered Aug 03 '21 at 14:21

user3091668

2,230
6
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Extend range in both directions

4 Answers4