 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
...         ...                  ... ...       ...         ...

> 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@huskers.unl.edu

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