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Question: IRanges findOverlaps potential bug?
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4.3 years ago by
Arun20
Germany
Arun20 wrote:
Hi BioC list, I just came across something I believe is an unexpected result (potential bug) in IRanges. I'm using the development version, but the same happens in stable version as well. My sincerest apologies if it's a misunderstanding on my part. In the example below, I'd expect the result for 'ans2' to be a vector of length 6, but with all values = 4L instead of 3L. By looking at ?findOverlaps, it seems like select should work with all values of argument 'type'. ## code require(IRanges) ii = IRanges(start=3L, end=c(5L, 5L, 16L, 20L, 24L, 47L)) #?IRanges of length 6 #?? ? start end width #?[1] ? ? 3 ? 5 ? ? 3 #?[2] ? ? 3 ? 5 ? ? 3 #?[3] ? ? 3 ?16 ? ?14 #?[4] ? ? 3 ?20 ? ?18 #?[5] ? ? 3 ?24 ? ?22 # [6] ? ? 3 ?47 ? ?45 xx = IRanges(start=c(1L,2L,3L,3L,6L), end=c(646L, 481L, 672L, 1037L, 153L)) #?IRanges of length 5 #?? ? start ?end width #?[1] ? ? 1 ?646 ? 646 #?[2] ? ? 2 ?481 ? 480 #?[3] ? ? 3 ?672 ? 670 #?[4] ? ? 3 1037 ?1035 # [5] ? ? 6 ?153 ? 148 ## works fine, as expected ans1 = as.data.frame(findOverlaps(ii, xx, type="start", select="all")) # ? ?query subject # 1 ? ? ?1 ? ? ? 3 # 2 ? ? ?1 ? ? ? 4 # 3 ? ? ?2 ? ? ? 3 # 4 ? ? ?2 ? ? ? 4 # 5 ? ? ?3 ? ? ? 3 # 6 ? ? ?3 ? ? ? 4 # 7 ? ? ?4 ? ? ? 3 # 8 ? ? ?4 ? ? ? 4 # 9 ? ? ?5 ? ? ? 3 # 10 ? ? 5 ? ? ? 4 # 11 ? ? 6 ? ? ? 3 # 12 ? ? 6 ? ? ? 4 ## potential bug? ans2 = findOverlaps(ii, xx, type="start", select="last") # [1] 3 3 3 3 3 3 This seems like a bug to me. If not, could you please explain? Thank you. --- sessionInfo() # R version 3.1.1 (2014-07-10) #?Platform: x86_64-apple-darwin10.8.0 (64-bit) #?locale: #?[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 #?attached base packages: #?[1] parallel ?graphics ?grDevices datasets ?stats ? ? utils ? ? methods ? base ? ?? #?other attached packages: #?[1] IRanges_1.99.24 ? ? S4Vectors_0.1.2 ? ? BiocGenerics_0.11.4 bit64_0.9-4 ? ? ? ? #?[5] bit_1.1-12 ? ? ? ?? #?loaded via a namespace (and not attached): #?[1] stats4_3.1.1 tools_3.1.1? Arun [[alternative HTML version deleted]]
modified 4.3 years ago by Michael Lawrence10k • written 4.3 years ago by Arun20
0
4.3 years ago by
United States
Michael Lawrence10k wrote:
Thanks. Fixed in 1.99.25. We had never actually implemented select="last". On Thu, Aug 28, 2014 at 1:09 PM, Arunkumar Srinivasan <aragorn168b at="" gmail.com=""> wrote: > Hi BioC list, > > I just came across something I believe is an unexpected result (potential > bug) in IRanges. I'm using the development version, but the same happens in > stable version as well. My sincerest apologies if it's a misunderstanding > on my part. > > In the example below, I'd expect the result for 'ans2' to be a vector of > length 6, but with all values = 4L instead of 3L. By looking at > ?findOverlaps, it seems like select should work with all values of > argument 'type'. > > ## code > require(IRanges) > ii = IRanges(start=3L, end=c(5L, 5L, 16L, 20L, 24L, 47L)) > # IRanges of length 6 > # start end width > # [1] 3 5 3 > # [2] 3 5 3 > # [3] 3 16 14 > # [4] 3 20 18 > # [5] 3 24 22 > # [6] 3 47 45 > > xx = IRanges(start=c(1L,2L,3L,3L,6L), end=c(646L, 481L, 672L, 1037L, 153L)) > # IRanges of length 5 > # start end width > # [1] 1 646 646 > # [2] 2 481 480 > # [3] 3 672 670 > # [4] 3 1037 1035 > # [5] 6 153 148 > > ## works fine, as expected > ans1 = as.data.frame(findOverlaps(ii, xx, type="start", select="all")) > # query subject > # 1 1 3 > # 2 1 4 > # 3 2 3 > # 4 2 4 > # 5 3 3 > # 6 3 4 > # 7 4 3 > # 8 4 4 > # 9 5 3 > # 10 5 4 > # 11 6 3 > # 12 6 4 > > ## potential bug? > ans2 = findOverlaps(ii, xx, type="start", select="last") > # [1] 3 3 3 3 3 3 > > This seems like a bug to me. If not, could you please explain? Thank you. > > --- > > sessionInfo() > # R version 3.1.1 (2014-07-10) > # Platform: x86_64-apple-darwin10.8.0 (64-bit) > > # locale: > # [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > # attached base packages: > # [1] parallel graphics grDevices datasets stats utils methods > base > > # other attached packages: > # [1] IRanges_1.99.24 S4Vectors_0.1.2 BiocGenerics_0.11.4 > bit64_0.9-4 > # [5] bit_1.1-12 > > # loaded via a namespace (and not attached): > # [1] stats4_3.1.1 tools_3.1.1 > > Arun > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]