[Bioc-sig-seq] Coercion of GenomeData to RangedData

[Dario Strbenac]

Here is a string representation :

> str(rs)
Formal class 'GenomeData' [package "BSgenome"] with 4 slots
  ..@ listData       :List of 25
  .. ..$ chr1 :List of 2
  .. .. ..$ -: int [1:375671] 184 191 194 507 511 522 526 545 551 562 ...
  .. .. ..$ +: int [1:376001] 152 234 244 248 277 440 450 451 452 458 ...
  .. ..$ chr2 :List of 2
  .. .. ..$ -: int [1:331924] 384 392 570 660 716 720 729 731 741 747 ...
  .. .. ..$ +: int [1:332302] 234 283 535 590 659 663 682 704 710 724 ...
  .. ..$ chr3 :List of 2
  .. .. ..$ -: int [1:212665] 46758 50637 50654 50691 50703 50723 50735 50789 54970 55050 ...
  .. .. ..$ +: int [1:212274] 38885 50529 50545 50551 50581 50582 50583 50630 50695 54859 ...

   ...            ...              ... 

  ..@ elementMetadata: NULL
  ..@ elementType    : chr "ANY"
  ..@ metadata       :List of 3
  .. ..$ organism       : NULL
  .. ..$ provider       : NULL
  .. ..$ providerVersion: NULL

---- Original message ----
>Date: Mon, 18 Oct 2010 19:48:37 -0700
>From: Michael Lawrence <lawrence.michael at gene.com>  
>Subject: Re: [Bioc-sig-seq] Coercion of GenomeData to RangedData  
>To: D.Strbenac at garvan.org.au
>Cc: bioc-sig-sequencing at r-project.org
>
>   That coercion only works if the elements of your
>   GenomeData are coercible to RangedData (which after
>   coercion are combined into a single RangedData). So
>   it would be good to know what's in your GenomeData.
>   If each element is a list, as your error message
>   suggests, it won't work, as there really is no way
>   to convert a list to a RangedData.
>
>   Michael
>
>   On Mon, Oct 18, 2010 at 7:00 PM, Dario Strbenac
>   <D.Strbenac at garvan.org.au> wrote:
>
>     Hello,
>
>     This conversion used to work before but it seems
>     like it doesn't any longer.
>
>     > summary(rs)
>        Length      Class       Mode
>            25 GenomeData         S4
>     > as(rs, "RangedData")
>     Error in FUN(X[[1L]], ...) :
>      no method or default for coercing "list" to
>     "RangedData"
>     > sessionInfo()
>     R version 2.12.0 (2010-10-15)
>     Platform: x86_64-pc-mingw32/x64 (64-bit)
>
>     locale:
>     [1] LC_COLLATE=English_Australia.1252
>      LC_CTYPE=English_Australia.1252  
>      LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>     [5] LC_TIME=English_Australia.1252
>
>     attached base packages:
>     [1] stats     graphics  grDevices utils    
>     datasets  methods   base
>
>     other attached packages:
>     [1] BSgenome_1.18.0     Biostrings_2.18.0  
>     GenomicRanges_1.2.0 IRanges_1.8.0
>
>     loaded via a namespace (and not attached):
>     [1] Biobase_2.8.0
>
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