Entering edit mode
Stephanie M. Gogarten
▴
890
@stephanie-m-gogarten-5121
Last seen 16 months ago
University of Washington
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
