Hi, I just ran into this bug using the GRanges method of nearest (which calls precede & follow) with ignore.strand=TRUE > nearest(GRanges("chr1", IRanges(1, width=1)), GRanges("chr1", IRanges(10, width=1)), ignore.strand=TRUE) Error in strand(x) <- strand(subject) <- "+" : object 'x' not found And tracked it down to here > GenomicRanges:::.findPrecedeFollow_GRanges function (query, subject, select, ignore.strand, where = c("precede", "follow")) { leftOf <- "precede" == match.arg(where) if (ignore.strand) strand(x) <- strand(subject) <- "+" strand(x) should be strand(query) > sessionInfo() R version 2.15.0 (2012-03-30) 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=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=C 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] xtable_1.7-0 BSgenome.Hsapiens.UCSC.hg19_1.3.17 [3] BSgenome_1.24.0 Biostrings_2.24.1 [5] multicore_0.1-7 rtracklayer_1.16.3 [7] Repitools_1.2.0 GenomicRanges_1.8.7 [9] IRanges_1.14.4 BiocGenerics_0.2.0 [11] limma_3.12.1 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 RCurl_1.91-1 Rsamtools_1.8.5 stats4_2.15.0 [5] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 zlibbioc_1.2.0 Thanks, Aaron --- Aaron Statham Postgraduate Scholar, Cancer Epigenetics Garvan Institute of Medical Research Tel: (02) 9295 8386 384 Victoria St Darlinghurst 2010 Fax: (02) 9825 8316 NSW Australia email: a.statham at garvan.org.au

Hi Aaron, Thanks for catching this. Now fixed in GenomicRanges 1.8.8 in release and 1.9.35 in devel. Valerie On 07/18/2012 10:17 PM, a.statham at garvan.org.au wrote: > Hi, > > I just ran into this bug using the GRanges method of nearest > (which calls precede& follow) with ignore.strand=TRUE > >> nearest(GRanges("chr1", IRanges(1, width=1)), > GRanges("chr1", IRanges(10, width=1)), ignore.strand=TRUE) > Error in strand(x)<- strand(subject)<- "+" : object 'x' not > found > > > And tracked it down to here > >> GenomicRanges:::.findPrecedeFollow_GRanges > function (query, subject, select, ignore.strand, where = > c("precede", > "follow")) > { > leftOf<- "precede" == match.arg(where) > if (ignore.strand) > strand(x)<- strand(subject)<- "+" > > strand(x) should be strand(query) > >> sessionInfo() > R version 2.15.0 (2012-03-30) > 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=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C 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] xtable_1.7-0 > BSgenome.Hsapiens.UCSC.hg19_1.3.17 > [3] BSgenome_1.24.0 Biostrings_2.24.1 > [5] multicore_0.1-7 rtracklayer_1.16.3 > [7] Repitools_1.2.0 GenomicRanges_1.8.7 > [9] IRanges_1.14.4 BiocGenerics_0.2.0 > [11] limma_3.12.1 > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1 RCurl_1.91-1 Rsamtools_1.8.5 > stats4_2.15.0 > [5] tcltk_2.15.0 tools_2.15.0 XML_3.9-4 > zlibbioc_1.2.0 > > > Thanks, > Aaron > > --- > Aaron Statham > Postgraduate Scholar, Cancer Epigenetics > Garvan Institute of Medical Research Tel: (02) 9295 8386 > 384 Victoria St Darlinghurst 2010 Fax: (02) 9825 8316 > NSW Australia email: a.statham at garvan.org.au > > _______________________________________________ > 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