Entering edit mode
Bill Gibb
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20
@bill-gibb-5755
Last seen 10.2 years ago
Hello,
I noticed that when applying set operations to GRanges objects, the
returned range is reduced (by default), e.g.
r1 <- GRanges(seqnames=c(1,1,1),
ranges=IRanges(start=c(1,3,5), end=c(1,3,5)), strand='*')
length(r1)
r2 <- GRanges(seqnames=c(1,1,1),
ranges=IRanges(start=c(1,3,4), end=c(1,3,4)), strand='*')
length(r2)
r3 <- union(r1,r2)
length(r3)
sum(width(ranges(r3)))
Both r1 and r2 have length 3, whereas r3 has length 2, due to the
implicit reduce applied to the result of union(). I can see that
reducing the ranges would normally be desired when applying set
operations, however there are occasions when one might want to keep a
list of singleton ranges (e.g. when sub-sampling at the genomic
coordinate level). Is there a way to suppress the reduce() operation
when applying set operations to GRanges? Something like union(r1, r2,
reduce.ranges=FALSE) would be nice.
I also tried:
resize(r3,width=1)
however it appears to simply truncate multi-base sequences.
Thank you.
Bill Gibb
Genomic Health, Inc.
Redwood City, CA
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Dear Herve,
I have a similar problem, but this time with setdiff: I have two GRanges objects, of which one is the genome in 100k bins (bin.grange):
> bin.grange GRanges object with 30946 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] 1 [ 0, 100000] * [2] 1 [100000, 200000] * [3] 1 [200000, 300000] * [4] 1 [300000, 400000] * [5] 1 [400000, 500000] * ... ... ... ... [30942] Y [58800000, 58900000] * [30943] Y [58900000, 59000000] * [30944] Y [59000000, 59100000] * [30945] Y [59100000, 59200000] * [30946] Y [59200000, 59300000] * ------- seqinfo: 24 sequences from an unspecified genome; no seqlengthsThe other GRange is a GRanges object (called peak.grange) that I would like to remove from bin.grange:
> peak.grange GRanges object with 77526 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] 1 [721223, 721768] * [2] 1 [808497, 809975] * [3] 1 [879120, 879638] * [4] 1 [888891, 889692] * [5] 1 [891102, 891624] * ... ... ... ... [77522] Y [58979198, 58979974] * [77523] Y [58980148, 58981354] * [77524] Y [58981384, 58982127] * [77525] Y [58982821, 58983574] * [77526] Y [59001388, 59001995] * ------- seqinfo: 25 sequences from an unspecified genome; no seqlengthsSimilar to the above example, a setdiff() between the two GRanges will automatically evoke the reduce method on the result:
> setdiff(bin.grange, peak.grange) GRanges object with 77529 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] 1 [ 1, 721222] * [2] 1 [721769, 808496] * [3] 1 [809976, 879119] * [4] 1 [879639, 888890] * [5] 1 [889693, 891101] * ... ... ... ... [77525] Y [58979975, 58980147] * [77526] Y [58981355, 58981383] * [77527] Y [58982128, 58982820] * [77528] Y [58983575, 59001387] * [77529] Y [59001996, 59300000] * ------- seqinfo: 25 sequences from an unspecified genome; no seqlengthsI would, however, like to maintain the 100k binned nature of the result. Is there a way to avoid evoking the reduce method?
Thank you very much,
Thomas Kuilman
--------------------------------------------------
Thomas Kuilman, PhD
Department of Molecular Oncology
Netherlands Cancer Institute
1066 CX Amsterdam
The Netherlands
Just after writing this post I found out how to get around this problem and I thought I should share this piece of code (see below). The trick I used is to use split() to split odd and even indices over two separate GRanges objects in a GRangesList. The example code below does setdiff(bin.grange, peak.grange) without reducing the result:
## Split into GRangesList object based on index: odd go in one, even in another element bin.grange <- split(bin.grange, rep_len(c(1, 2), length.out = length(bin.grange))) ## Apply the setdiff on the independent GRanges objects in the GRangesList bin.grange <- lapply(bin.grange, function(x) { setdiff(x, peak.grange) }) ## Merge into one GRanges object again bin.grange <- c(bin.grange[[1]], bin.grange[[2]]) ## Order ranges bin.grange <- bin.grange[order(bin.grange)]Regards,
Thomas