On Thu, Apr 1, 2010 at 7:22 AM, Martin Morgan <[email protected]> wrote:
> On 04/01/2010 07:12 AM, Michael Lawrence wrote: > > 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? > > Currently GRanges thinks of strand as '+', '-', '*', whereas IRanges > allows NA as well (hence the error) so coercing NA to * represents a > decision on the part of the investigator that '*' (strand irrelevant) is > synonymous with NA (no information about strand available). Part of the > motivation for this current state of affairs is that the use case for > both NA and * were unclear, but course corrections welcome. > > Ok. I guess one could think of the coercion of a RangedData missing a 'strand' column to a GRanges as an equivalent statement, since GRanges requires strand information. If that doesn't sound reasonable, a better error message will help avoid questions like this in the future. Michael > 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 > >>> [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 > >> > > > > > -- > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
