problem with TxDb.Hsapiens.UCSC.hg19.knownGene
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0
Entering edit mode
l.selfors • 0
@lselfors-14063
Last seen 4.0 years ago

Hi, I just reinstalled TxDb.Hsapiens.UCSC.hg19.knownGene and it does not function. When I load the package, the TxDb object looks fine, but applying any function to it fails.  For example genes() gives character(0) and seqlevels() gives an empty GRanges object:

 

 

> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene # abbreviate
> genes(txdb)
GRanges object with 0 ranges and 1 metadata column:
   seqnames    ranges strand |     gene_id
      <Rle> <IRanges>  <Rle> | <character>
  -------
  seqinfo: no sequences
> seqlevels(txdb)
character(0)
>
> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>
> txdb = TxDb.Hsapiens.UCSC.hg19.knownGene
> txdb
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: UCSC
# Genome: hg19
# Organism: Homo sapiens
# Taxonomy ID: 9606
# UCSC Table: knownGene
# Resource URL: http://genome.ucsc.edu/
# Type of Gene ID: Entrez Gene ID
# Full dataset: yes
# miRBase build ID: GRCh37
# transcript_nrow: 82960
# exon_nrow: 289969
# cds_nrow: 237533
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2015-10-07 18:11:28 +0000 (Wed, 07 Oct 2015)
# GenomicFeatures version at creation time: 1.21.30
# RSQLite version at creation time: 1.0.0
# DBSCHEMAVERSION: 1.1
> genes(txdb)
GRanges object with 0 ranges and 1 metadata column:
   seqnames    ranges strand |     gene_id
      <Rle> <IRanges>  <Rle> | <character>
  -------
  seqinfo: no sequences
> seqlevels(txdb)
character(0)

 

 

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Mavericks 10.9.5

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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.4.0                      TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.26.4                 
 [4] AnnotationDbi_1.36.2                    Biobase_2.34.0                          GenomicRanges_1.26.4                   
 [7] GenomeInfoDb_1.10.3                     IRanges_2.8.2                           S4Vectors_0.12.2                       
[10] BiocGenerics_0.20.0                     BiocInstaller_1.24.0                    biomaRt_2.30.0                         
[13] reshape2_1.4.2                          gplots_3.0.1                            RColorBrewer_1.1-2                     
[16] heatmap.plus_1.3                       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               plyr_1.8.4                 XVector_0.14.1             bitops_1.0-6               tools_3.3.2               
 [6] zlibbioc_1.20.0            digest_0.6.12              bit_1.1-12                 lattice_0.20-35            RSQLite_2.0               
[11] memoise_1.1.0              tibble_1.3.4               pkgconfig_2.0.1            rlang_0.1.2                Matrix_1.2-11             
[16] DBI_0.7                    rtracklayer_1.34.2         stringr_1.2.0              Biostrings_2.42.1          gtools_3.5.0              
[21] caTools_1.17.1             grid_3.3.2                 bit64_0.9-7                BiocParallel_1.8.2         XML_3.98-1.9              
[26] gdata_2.18.0               blob_1.1.0                 magrittr_1.5               GenomicAlignments_1.10.1   Rsamtools_1.26.2          
[31] SummarizedExperiment_1.4.0 KernSmooth_2.23-15         stringi_1.1.5              RCurl_1.95-4.8            

 

I'd appreciate some help on this.  Thanks.

Laura

 

 

TxDb.Hsapiens.UCSC.hg19.knownGene • 593 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 19 hours ago
United States

We don't support old versions of Bioconductor, so the first thing to do is upgrade to R-3.4.1 and the current version of Bioconductor. That will probably fix things, but let us know if you are still having problems.

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