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Question: rtracklayer browseGenome error with named ranges
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gravatar for Stephanie M. Gogarten
2.8 years ago by
University of Washington
Stephanie M. Gogarten560 wrote:

I found that browseGenome in the rtracklayer package fails if the ranges supplied have names. This works:

> ir <- IRanges(20000, 50000)
> track <- GRangesForUCSCGenome("hg19", chrom="chr22", ranges=ir)
> browseGenome(track)
A genome browser session of class 'UCSCSession' with 1 views and 181 tracks

This does not work:

> ir <- IRanges(20000, 50000, names="a")
> track <- GRangesForUCSCGenome("hg19", chrom="chr22", ranges=ir)
> browseGenome(track)
Error in FUN(extractROWS(X, i), ...) : Invalid chromosomes for hg19: a


> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
[1] XVector_0.9.3         rtracklayer_1.29.21   GenomicRanges_1.21.21
[4] GenomeInfoDb_1.5.13   IRanges_2.3.18        S4Vectors_0.7.15     
[7] BiocGenerics_0.15.6  

loaded via a namespace (and not attached):
 [1] XML_3.98-1.3               Rsamtools_1.21.16         
 [3] Biostrings_2.37.8          GenomicAlignments_1.5.13  
 [5] bitops_1.0-6               futile.options_1.0.0      
 [7] zlibbioc_1.15.0            futile.logger_1.4.1       
 [9] lambda.r_1.1.7             BiocParallel_1.3.51       
[11] tools_3.2.1                Biobase_2.29.1            
[13] RCurl_1.95-4.7             compiler_3.2.1            
[15] SummarizedExperiment_0.3.3

 

ADD COMMENTlink modified 2.8 years ago by Michael Lawrence10.0k • written 2.8 years ago by Stephanie M. Gogarten560
0
gravatar for Michael Lawrence
2.8 years ago by
Michael Lawrence10.0k
United States
Michael Lawrence10.0k wrote:

Thanks, cruft left over from when it was all based on RangedData. Fixed in devel (1.29.23).

ADD COMMENTlink written 2.8 years ago by Michael Lawrence10.0k
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