[Bioc-sig-seq] GenomicFeatures, error in type conversion RangeData to GRanges

[Martin Morgan]

On 03/31/2010 07:11 PM, pterry at huskers.unl.edu wrote:
>  Dear bioc-sig-sequencing,
> 
> I would like to annotate chip-seq peaks for the arabidopsis genome.  In trying to work thru the GenomicFeatures vignette dated 03/27/10, I need to convert my ChIPSeq peaks from a RangedData object to a GRanges object.  In a recent, but previous Bioconductor development version, the conversion with this particular RangedData object worked fine.
> 
> In this more recent Bioconductor development version, I get the following error message:
> 
>> gr_ChSeqPks <- as(rd0_chr1_s_8_trt_vs_INPctl, "GRanges")
> Error in validObject(.Object) :
>   invalid class "GRanges" object: slot 'strand' contains missing values
>> rd0_chr1_s_8_trt_vs_INPctl
> RangedData with 57 rows and 2 value columns across 1 space
>           space               ranges   |     ARAB8 ARAB7INPCTL
>     <character>            <IRanges>   | <integer>   <integer>
> 1          chr1   [ 617092,  617094]   |        24           0
> 2          chr1   [1808262, 1808262]   |         8           0
> 3          chr1   [3889445, 3889452]   |        64           0
> 4          chr1   [4404410, 4404410]   |         8           0
> 5          chr1   [7081127, 7081127]   |         8           0
> 6          chr1   [7128574, 7128581]   |        64           0
> 7          chr1   [7128592, 7128649]   |       464           0
> 8          chr1   [7530777, 7530781]   |        40           0
> 9          chr1   [7530784, 7530786]   |        24           0
> ...         ...                  ... ...       ...         ...

Hi,

> rd = RangedData(IRanges(1, 10))
> as(rd, "GRanges")
Error in validObject(.Object) :
  invalid class "GRanges" object: slot 'strand' contains missing values
> rd[["strand"]] = "*"
> as(rd, "GRanges")
GRanges with 1 range and 0 elementMetadata values
    seqnames    ranges strand |
       <Rle> <IRanges>  <Rle> |
[1]        1   [1, 10]      * |

seqlengths
 1
NA

Martin

> 
>> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-03-30 r51506)
> x86_64-unknown-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.3.5         GenomicFeatures_0.5.0 GenomicRanges_0.1.0
> [4] IRanges_1.5.73
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.7.5      Biostrings_2.15.26 BSgenome_1.15.20   DBI_0.2-5
> [5] RCurl_1.3-1        RSQLite_0.8-4      rtracklayer_1.7.11 tools_2.12.0
> [9] XML_2.8-1
>>
> 
> 
> Thanks,
> P. Terry
> pterry at huskers.unl.edu
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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