Hello, I'm encountering some strange behaviour. If I do psetdiff with 2 GRangesLists that I have, it gives an error, but if I split the GRangesLists into 2 parts I can't get the error to happen. Any ideas ?
> length(gene.juncts) [1] 36693 > length(gene.exons) [1] 36693 > intronics <- psetdiff(gene.juncts, gene.exons) Error in gaps(union(gaps(x, end = seqlengths), y, ignore.strand = ignore.strand), : error in evaluating the argument 'x' in selecting a method for function 'gaps': Error in sort.list(runValue(x), na.last = na.last, decreasing = decreasing, : too large a range of values in 'x' > intronics <- psetdiff(gene.juncts[1:20000], gene.exons[1:20000]) > intronics <- psetdiff(gene.juncts[20001:length(gene.juncts)], > gene.exons[20001:length(gene.exons)]) > To help with troubleshooting, the two GRangesLists are available for download. http://129.94.136.7/file_dump/dario/testPsetDiff.RData (3.7 MB) > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.4.1 GenomicRanges_1.4.6 IRanges_1.10.4 loaded via a namespace (and not attached): [1] Biobase_2.11.10 biomaRt_2.7.2 Biostrings_2.19.18 [4] BSgenome_1.19.6 DBI_0.2-5 RCurl_1.6-1 [7] RSQLite_0.9-4 rtracklayer_1.11.12 XML_3.4-0 -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing