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
[email protected]
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