On Thu, Apr 1, 2010 at 7:09 AM, Martin Morgan <[email protected]> wrote:
> On 03/31/2010 07:11 PM, [email protected] 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 > > Shouldn't the coerce function just do this automatically? > > > >> 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] > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
