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 <julie....@umassmed.edu> 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
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
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