Vince, Michael, Thanks both of you. It is good to know that the devel version works correctly. I guess it is always a good idea to get the most recent devel version. Have a great weekend! Xiwei ________________________________ From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Sat 1/30/2010 8:38 PM To: Vincent Carey Cc: Wu, Xiwei; Michael Lawrence; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] FindOverlaps Problem On Sat, Jan 30, 2010 at 1:33 PM, Vincent Carey <stvjc@channing.harvard.edu> wrote: ah -- my result was with devel, and in fact it does not agree with yours, but it seems correct in this instance. I think there was a bug in the as.matrix() method on the overlap result that was fixed relatively recently. This probably explains the difference. Thanks for looking into this Vince. Michael > sessionInfo() R version 2.11.0 Under development (unstable) (2010-01-07 r50940) i386-apple-darwin9.8.0 locale: [1] C attached base packages: [1] grid stats graphics grDevices datasets tools utils [8] methods base other attached packages: [1] GenomeGraphs_1.7.1 biomaRt_2.3.0 leeBamSet_0.0.8 [4] Rsamtools_0.1.24 BSgenome_1.15.4 Biostrings_2.15.18 [7] IRanges_1.5.31 org.Sc.sgd.db_2.3.5 RSQLite_0.7-3 [10] DBI_0.2-4 AnnotationDbi_1.9.0 Biobase_2.7.0 [13] weaver_1.13.0 codetools_0.2-2 digest_0.4.1 loaded via a namespace (and not attached): [1] RCurl_1.3-0 XML_2.6-0 On Sat, Jan 30, 2010 at 4:30 PM, Vincent Carey <stvjc@channing.harvard.edu> wrote: > It seems to me that it is working correctly but you can't assume that > the order of ranges at time of construction serves as the order in the > ultimate object. A lexicographic ordering by space names is used. > Challenging to interpret but if you look at the values of a and b > before interpreting your findOverlaps result it starts to make sense. > >> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, > 7), sep="")) >> a > RangedData with 7 rows and 0 value columns across 7 spaces > space ranges | > <character> <iranges> | > 1 chr10 [1, 10] | > 2 chr2 [1, 10] | > 3 chr3 [1, 10] | > 4 chr5 [1, 10] | > 5 chr6 [1, 10] | > 6 chr7 [1, 10] | > 7 chr9 [1, 10] | >> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3 > , "X"), sep="")) >> b > RangedData with 7 rows and 0 value columns across 7 spaces > space ranges | > <character> <iranges> | > 1 chr10 [1, 10] | > 2 chr18 [1, 10] | > 3 chr2 [1, 10] | > 4 chr21 [1, 10] | > 5 chr3 [1, 10] | > 6 chr5 [1, 10] | > 7 chrX [1, 10] | >> findOverlaps(a,b) > RangesMatchingList of length 7 > names(7): chr10 chr2 chr3 chr5 chr6 chr7 chr9 >> as.matrix(.Last.value) > query subject > [1,] 1 1 > [2,] 2 3 > [3,] 3 5 > [4,] 4 6 > > > On Sat, Jan 30, 2010 at 1:09 PM, Wu, Xiwei <xwu@coh.org> wrote: >> Michael, >> >> Here is one example. Please let me know if I have missed anything. Thanks. >> >>> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) >>> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3, "X"), sep="")) >>> as.matrix(findOverlaps(a, a)) >> query subject >> [1,] 1 1 >> [2,] 2 2 >> [3,] 3 3 >> [4,] 4 4 >> [5,] 5 5 >> [6,] 6 6 >> [7,] 7 7 >>> as.matrix(findOverlaps(a, b)) >> query subject >> [1,] 1 1 >> [2,] 2 3 >> [3,] 3 5 >> [4,] 4 5 >>> a[4] >> RangedData with 1 row and 0 value columns across 1 space >> space ranges | >> <character> <iranges> | >> 1 chr5 [1, 10] | >>> b[5] >> RangedData with 1 row and 0 value columns across 1 space >> space ranges | >> <character> <iranges> | >> 1 chr3 [1, 10] | >>> sessionInfo() >> R version 2.10.0 (2009-10-26) >> x86_64-unknown-linux-gnu >> >> 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=C >> [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] rtracklayer_1.6.0 RCurl_1.3-1 >> [3] bitops_1.0-4.1 BSgenome.Hsapiens.UCSC.hg18_1.3.15 >> [5] ShortRead_1.4.0 lattice_0.17-26 >> [7] BSgenome_1.14.0 Biostrings_2.14.0 >> [9] IRanges_1.4.0 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1 tools_2.10.0 XML_2.6-0 >> >> >> Xiwei >> ________________________________________ >> From: Michael Lawrence [mailto:lawrence.michael@gene.com] >> Sent: Friday, January 29, 2010 1:13 PM >> To: Wu, Xiwei >> Cc: bioconductor@stat.math.ethz.ch >> Subject: Re: [BioC] FindOverlaps Problem >> >> Need input... what is the expected result? and what actually happened? sessionInfo()... >> On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <xwu@coh.org> wrote: >> Dear all, >> >> I found that the findOverlaps function does not work properly if the >> space levels do not match exactly between subject and query. Has anyone >> noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is >> this problem being fixed in the developmental version? >> >> Thanks. >> >> Xiwei >> >> >> --------------------------------------------------------------------- >> SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:10}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]]