[Bioc-devel] bug in GRanges show method

[Hervé Pagès]

Thanks Florian for the report. We'll fix.

H.

On 04/25/2012 12:12 AM, Hahne, Florian wrote:
> I found a little bug in the GRanges show method when using non-standard
> names in the elementMetadata DataFrame:
> foo<- GRanges(seqnames=rep("a", 3), ranges=IRanges(start=c(1,100, 1000),
> width=10))
> ds<- DataFrame("450-2"=1:3, "test"=5:7)
> values(foo)<- ds
> foo
> GRanges with 3 ranges and 2 elementMetadata cols:
> Error: identical(colnames(classinfo), colnames(out)) is not TRUE
>
> The problem is that in the .makeNakedMatFromGenomicRanges function a
> data.frame is being created without check.names=FALSE, so the
>
>
> non-standard colnames are converted and do not match the original colnames
> of the DataFrame anymore. The fix is trivial:
>
> .makeNakedMatFromGenomicRanges<- function(x)
> {
>      lx<- length(x)
>      nc<- ncol(elementMetadata(x))
>      ans<- cbind(seqnames=as.character(seqnames(x)),
>                   ranges=IRanges:::showAsCell(ranges(x)),
>                   strand=as.character(strand(x)))
>      if (nc>  0L) {
>          tmp<- do.call(data.frame, c(lapply(elementMetadata(x),
>                                            IRanges:::showAsCell),
> check.names=FALSE))
>          ans<- cbind(ans, `|`=rep.int("|", lx), as.matrix(tmp))
>      }
>      ans
> }
>
> Would be great if someone could fix that.
>
> Florian
>
> R Under development (unstable) (2012-04-16 r59045)
> Platform: x86_64-unknown-linux-gnu/x86_64 (64-bit)
>
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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] GenomicRanges_1.9.7 IRanges_1.15.4      BiocGenerics_0.3.0
> [4] BiocInstaller_1.5.7
>
> loaded via a namespace (and not attached):
> [1] stats4_2.16.0 tools_2.16.0
>
>
>
>
>
>
> Florian Hahne
> Novartis Institute For Biomedical Research
> Translational Sciences / Preclinical Safety / PCS Informatics
> Expert Data Integration and Modeling Bioinformatics
> CHBS, WKL-135.2.26
> Novartis Institute For Biomedical Research, Werk Klybeck
> Klybeckstrasse 141
> CH-4057 Basel
> Switzerland
> Phone: +41 61 6967127
> Email : florian.hahne at novartis.com
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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