Your statement is true except in the case where the query and subject are the same (original discussion below). When query and subject are the same (or contain >=1 of the same ranges) nearest() should choose self-hits. precede() and follow() will never select self-hits because they do not 'precede' or 'follow' them. These unit tests may help further explain the behavior we are expecting for "+", "-" and "*". r <- IRanges(c(1,5,10), c(2,7,12)) g <- GRanges("chr1", r, "+") checkEquals(precede(r), precede(g)) checkEquals(follow(r), follow(g)) checkEquals(nearest(r), nearest(g)) g <- GRanges("chr1", r, "-") checkEquals(follow(r), precede(g)) checkEquals(precede(r), follow(g)) checkEquals(nearest(r), nearest(g)) g <- GRanges("chr1", r, "*") checkEquals(follow(g), precede(g)) checkEquals(nearest(r), follow(g)) checkEquals(follow(g), nearest(g)) Valerie On 07/04/2012 02:12 AM, James Perkins wrote: > Thanks a lot Valerie! > > So precede with "*" is analogous to nearest? Since the nearest will > also be preceding it either + or - direction? > > Jim > > On 3 July 2012 21:04, Valerie Obenchain<vobencha at="" fhcrc.org=""> wrote: >> Hi James, >> >> Thanks for the bug report. The nearest,GRanges method is currently not >> selecting any range that includes itself. It should behave like IRanges and >> excluded self hits when one argument is supplied but not when the same >> argument is both query and subject. I'll post back here when it is fixed. >> >> Here is an example that will help explain how '*' is treated as far as >> matching. For precede(), follow() and nearest() the '*' strand is treated as >> '+' and '-' when looking for potential matches. >> >>> q<- GRanges("chr1", IRanges(c(1, 3, 9), c(2, 7, 10))) >>> q >> GRanges with 3 ranges and 0 elementMetadata cols: >> seqnames ranges strand >> <rle> <iranges> <rle> >> [1] chr1 [1, 2] * >> [2] chr1 [3, 7] * >> [3] chr1 [9, 10] * >> --- >> seqlengths: >> chr1 >> NA >> >> ## The second range could be seen as preceding range 3 on '+' >> ## or preceding range 1 on '-'. Range 1 is closer so it is chosen. >> ## The third range precedes no range on '+' but precedes >> ## range 2 on '-' so range 2 is chosen. >>> precede(q) >> [1] 2 1 2 >>> precede(ranges(q)) >> [1] 2 3 NA >> >> ## When the strand is '+' GRanges and IRanges behave the same. >>> strand(q)<- "+" >>> precede(q) >> [1] 2 3 NA >>> precede(ranges(q)) >> [1] 2 3 NA >> >> ## When the strand is '-' GRanges treats the ranges as '-' but >> ## IRanges is unstranded so they are treated as '+'. >>> strand(q)<- "-" >>> precede(q) >> [1] NA 1 2 >>> precede(ranges(q)) >> [1] 2 3 NA >> >> Valerie >> >> >> On 07/03/12 10:58, James Perkins wrote: >>> Thanks, >>> >>> But it appears in the example (using GenomicRanges_1.8.7), the second >>> range is being excluded? I.e. 3-7 matches 5-6 (and 1-3) and thus is >>> >>>> subject2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(3, 5, 12), >>> +>> > c(3, 6, 12))) >>>> subject2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(3, 5, 12), >>>> c(3, 6, 12))) >>>> query2 >>> GRanges with 3 ranges and 0 elementMetadata cols: >>> seqnames ranges strand >>> <rle> <iranges> <rle> >>> [1] chr1 [1, 2] * >>> [2] chr1 [3, 7] * >>> [3] chr1 [9, 10] * >>> --- >>> seqlengths: >>> chr1 >>> NA >>>> subject2 >>> GRanges with 3 ranges and 0 elementMetadata cols: >>> seqnames ranges strand >>> <rle> <iranges> <rle> >>> [1] chr1 [ 3, 3] * >>> [2] chr1 [ 5, 6] * >>> [3] chr1 [12, 12] * >>> --- >>> seqlengths: >>> chr1 >>> NA >>>> nearest(query2, subject2) >>> [1] 1 3 3 >>>> nearest(subject2, query2) >>> [1] 1 1 3 >>> >>> Similarly >>> >>> nearest(query2, query2) >>> [1] 2 1 2 >>> >>> should surely be "1 2 3"? Or have I missed something? >>> >>> IRanges is as I would expect:> nearest(ranges(query2), ranges(subject2)) >>> [1] 1 1 3 >>> >>> >>> Jim >>> >>> >>> On 3 July 2012 19:40, Michael Lawrence<lawrence.michael at="" gene.com=""> wrote: >>>> The way IRanges works is that the self hits are excluded (by default) >>>> when >>>> only one argument is passed to nearest(). They should not be excluded >>>> when >>>> the same object is passed as both arguments. >>>> >>>> Michael >>>> >>>> On Tue, Jul 3, 2012 at 7:09 AM, James Perkins<jperkins at="" biochem.ucl.ac.uk=""> >>>> wrote: >>>>> Hi, >>>>> >>>>> I read this: >>>>> >>>>> https://mailman.stat.ethz.ch/pipermail/bioconductor/2012-June/04 6287.html >>>>> >>>>> However, after reading it I'm a little confused as to what the default >>>>> behaviour should be when using nearest with '*', and also how to get >>>>> back to what I believe was the previous, "IRanges" style behaviour. >>>>> >>>>> Is nearest on GRanges supposed to act like nearest on IRanges, or is >>>>> it instead supposed to return the nearest neighbour OTHER than the >>>>> query one? >>>>> >>>>> I.e. >>>>> >>>>> >>>>>> query<- IRanges(c(1, 3, 9), c(2, 7, 10)) >>>>>> subject<- IRanges(c(3, 5, 12), c(3, 6, 12)) >>>>>> nearest(query, subject) >>>>> [1] 1 1 3 >>>>> >>>>> Because, it seems to be behaving differently, i.e. returning the >>>>> neighbour only, i.e. >>>>> >>>>> >>>>>> query2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(1, 3, 9), >>>>>> c(2, 7, 10))) >>>>>> subject2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(3, 5, 12), >>>>>> c(3, 6, 12))) >>>>>> nearest(query2, subject2) >>>>> [1] 1 3 2 >>>>>> sessionInfo() >>>>> R version 2.15.1 (2012-06-22) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US LC_NUMERIC=C >>>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>>>> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >>>>> [7] LC_PAPER=C LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] GenomicRanges_1.8.7 IRanges_1.14.4 BiocGenerics_0.2.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] stats4_2.15.1 >>>>> >>>>> >>>>> However, what makes me confused is that the previous behaviour was like >>>>> IRanges: >>>>> >>>>>> query<- IRanges(c(1, 3, 9), c(2, 7, 10)) >>>>>> subject<- IRanges(c(3, 5, 12), c(3, 6, 12)) >>>>>> nearest(query, subject) >>>>> [1] 1 1 3 >>>>>> query2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(1, 1, 12), >>>>>> c(2, 7, 12))) >>>>>> subject2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(3, 5, 12), >>>>>> c(3, 6, 12))) >>>>>> nearest(query2, subject2) >>>>> [1] 1 1 3 >>>>>> sessionInfo() >>>>> R version 2.15.0 (2012-03-30) >>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=C LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] GenomicRanges_1.8.6 IRanges_1.14.3 BiocGenerics_0.2.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] stats4_2.15.0 >>>>> >>>>> >>>>> And in fact, this has always been the behaviour right? i.e.: for R >>>>> 2.13.1 >>>>> >>>>>> query<- IRanges(c(1, 3, 9), c(2, 7, 10)) >>>>>> subject<- IRanges(c(3, 5, 12), c(3, 6, 12)) >>>>>> nearest(query, subject) >>>>> [1] 1 1 3 >>>>>> query2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(1, 1, 12), >>>>>> c(2, 7, 12))) >>>>>> subject2<- GRanges(seqnames=rep('chr1',3),ranges=IRanges(c(3, 5, 12), >>>>>> c(3, 6, 12))) >>>>>> nearest(query2, subject2) >>>>> [1] 1 1 3 >>>>>> sessionInfo() >>>>> R version 2.13.1 (2011-07-08) >>>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] GenomicRanges_1.4.8 IRanges_1.10.6 >>>>> >>>>> >>>>> Is ignore.strand=TRUE intended to get the IRanges-like behaviour? >>>>> Because I have problems with this too: >>>>> >>>>> nearest(x = query2, subject = subject2, ignore.strand=TRUE) >>>>> Error in strand(x)<- strand(subject)<- "+" : object 'x' not found >>>>> >>>>> Thanks! >>>>> >>>>> Jim >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>> _______________________________________________ >>> 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 >>