Hi Kunbin, On Fri, Jul 22, 2011 at 2:11 AM, Kunbin Qu <k...@genomichealth.com> wrote: > Hi, > > I am trying to use "minoverlap" in the "countOverlaps" function to tune the > counts between entrez genes (annEx) and my reads (a Granges object: grNons). > But somehow it ran into a warning message, which unfortunately did not give > me why that parameter was not used. When "minoverlap" was not used, it worked > fine. Thanks.
I suspect this might be due to an outdate version of GenomicRanges? Can you show us your sessionInfo? Did you upgrade to the latest R/Bioconductor version as was previously suggested? In the latest version of GenomicRanges (only available with the latest version of bioconductor (which is only available with the latest version of R)), you'll find that countOverlaps can take a custom minoverlap parameter in the scenario you are using it in. HTH, -steve > > -Kunbin > > > grExNons<-countOverlaps(query=annEx, subject=grNons) > head(grExNons) > [1] 133 1 28 58 637 0 > grExNons<-countOverlaps(query=annEx, subject=grNons, minoverlap = 5L) > Warning message: > In countOverlaps(query = annEx, subject = grNons, minoverlap = 5L) : > 'minoverlap' argument is ignored > > hg19KG <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") > annEx<-exonsBy(hg19KG, "gene") > annEx > GRangesList of length 20545 > $1 > GRanges with 15 ranges and 2 elementMetadata values > seqnames ranges strand | exon_id exon_name > <Rle> <IRanges> <Rle> | <integer> <character> > [1] chr19 [58858174, 58858395] - | 253677 NA > [2] chr19 [58858719, 58859006] - | 253678 NA > [3] chr19 [58859832, 58860494] - | 253688 NA > ..... > >>grNons > GRanges with 27421835 ranges and 0 elementMetadata values > seqnames ranges strand | > <Rle> <IRanges> <Rle> | > [1] chr11 [ 48034060, 48034095] * | > [2] chr13 [103319962, 103319997] * | > [3] chr2 [198350561, 198350596] * | > [4] chr12 [ 41850809, 41850844] * | > [5] chr16 [ 89974865, 89974900] * | > [6] chr1 [172113839, 172113874] * | > [7] chr12 [111080272, 111080307] * | > [8] chr2 [179445437, 179445472] * | > [9] chr10 [119817069, 119817104] * | > ... ... ... ... ... > [27421827] chr17 [ 43334904, 43334939] * | > [27421828] chr6 [163903657, 163903692] * | > [27421829] chr18 [ 74737099, 74737134] * | > [27421830] chr13 [ 78311617, 78311652] * | > [27421831] chr4 [170541832, 170541867] * | > [27421832] chr13 [ 32601946, 32601981] * | > [27421833] chr3 [ 38420019, 38420054] * | > [27421834] chr8 [ 74561716, 74561751] * | > [27421835] chr3 [ 39319812, 39319847] * | > > seqlengths > chr1 chr10 chr11 chr12 chr13 chr14 ... chr6 chr7 chr8 chr9 chrX chrY > NA NA NA NA NA NA ... NA NA NA NA NA NA >> summary(width(grNons)) > Min. 1st Qu. Median Mean 3rd Qu. Max. > 18.00 36.00 36.00 35.85 36.00 36.00 >> > > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to postmas...@genomichealth.com and delete this message, along with > any attachments, from your computer. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
