[Bioc-sig-seq] RangedData: sorting problem

[Vincent Carey]

It seems to me this is a feature.  If you read the RangedData man page
(at least in R 2.11, which I checked) the underlying structures are
split by space.  Some reorderings are permitted, but the one that you
attempted leads to a situation in which rows from a given space are
not contiguous in the resulting row ordering.  This is not permitted.

On Tue, Mar 16, 2010 at 11:06 AM, Zhu, Julie <Julie.Zhu at 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
>
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