Thanks, Michael! Best regards,
Julie On 3/16/10 3:33 PM, "Michael Lawrence" <[email protected]> wrote: This is a limitation of the internal RangedData representation. The data must always be sorted by space (chromosome). Sorting by rownames in your case would violate that, so it's not allowed. There are new data structures entering into Bioconductor (GRanges and GRangesList) that support arbitrary sorting. If you really need to sort by rownames(), I would suggest using those instead of RangedData. In theory, RangedData could be fixed... On Tue, Mar 16, 2010 at 8:06 AM, Zhu, Julie <[email protected]> wrote: Hi, I am trying to sort a RangedData but encountered the following error. Here is a toy example to reproduce the error. Did I do something wrong? Thank you very much for your help! Best regards, Julie myPeak1 = RangedData(IRanges(start=c(967654, 2010897, 2496704, 3075869, 3123260 ,3857501,201089), end= c(967754, 2010997, 2496804, 3075969, 3123360 ,3857601,201089),names=c("Site1", "Site2", "Site3", "Site4", "Site5", "Site6", "site7")), space=c("1", "2", "3", "4", "5", "6","2")) myPeak1[order(rownames(myPeak1)),] Error in myPeak1[order(rownames(myPeak1)), ] : cannot combine 'i' row values from different spaces > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin8.11.1 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] Ringo_1.10.0 Matrix_0.999375-31 lattice_0.17-26 [4] limma_2.19.2 RColorBrewer_1.0-2 ChIPpeakAnno_1.2.4 [7] org.Hs.eg.db_2.3.6 GO.db_2.3.5 RSQLite_0.7-1 [10] DBI_0.2-4 AnnotationDbi_1.8.1 BSgenome.Ecoli.NCBI.20080805_1.3.16 [13] BSgenome_1.14.2 Biostrings_2.14.8 IRanges_1.4.9 [16] multtest_2.1.2 Biobase_2.5.5 biomaRt_2.1.0 loaded via a namespace (and not attached): [1] annotate_1.23.1 genefilter_1.25.7 MASS_7.3-3 RCurl_0.98-1 splines_2.10.0 survival_2.35-7 [7] tools_2.10.0 XML_2.3-0 xtable_1.5-6 ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
