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.
-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