I discovered that threeUTRsByTranscript does not work properly after invoking seqlevelsStyle as a setter function. Here is code to reproduce the issue:

refSeqDb = makeTxDbFromUCSC (
    "hg19",
    tablename = "refGene")
refSeqDb = keepStandardChromosomes (refSeqDb)
seqlevelsStyle (refSeqDb) = "NCBI"
threeUTRsByTranscript (refSeqDb)

The relevant output is:

> threeUTRsByTranscript (refSeqDb)
GRangesList object of length 0:
<0 elements>

-------
seqinfo: 25 sequences (1 circular) from hg19 genome

If I do not invoke seqlevelsStyle, then I instead obtain:

GRangesList object of length 39127:
$20
GRanges object with 1 range and 3 metadata columns:
      seqnames           ranges strand |   exon_id   exon_name exon_rank
         <Rle>        <IRanges>  <Rle> | <integer> <character> <integer>
  [1]     chr1 [879534, 879961]      + |        35        <NA>        14

$21
GRanges object with 1 range and 3 metadata columns:
      seqnames           ranges strand | exon_id exon_name exon_rank
  [1]     chr1 [900572, 901099]      + |      47      <NA>        12

$22
GRanges object with 1 range and 3 metadata columns:
      seqnames           ranges strand | exon_id exon_name exon_rank
  [1]     chr1 [909956, 910484]      + |      64      <NA>        15

...
<39124 more elements>
-------
seqinfo: 25 sequences (1 circular) from hg19 genome

as expected.

fiveUTRsByTranscript has the same issue, while intronsByTranscript functions as expected.

My session info is:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] C

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

other attached packages:
 [1] beanplot_1.2                               IlluminaHumanMethylation450kmanifest_0.4.0 goseq_1.20.0                               geneLenDataBase_1.4.0                     
 [5] BiasedUrn_1.06.1                           GO.db_3.1.2                                seqLogo_1.34.0                             fastcluster_1.1.16                        
 [9] GenomicAlignments_1.4.1                    Rsamtools_1.20.4                           BSgenome_1.36.3                            rtracklayer_1.28.10                       
[13] AnnotationHub_2.0.4                        minfi_1.14.0                               bumphunter_1.8.0                           locfit_1.5-9.1                            
[17] iterators_1.0.7                            foreach_1.4.2                              Biostrings_2.36.4                          XVector_0.8.0                             
[21] lattice_0.20-33                            FDb.InfiniumMethylation.hg19_2.2.0         org.Hs.eg.db_3.1.2                         RSQLite_1.0.0                             
[25] DBI_0.3.1                                  TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2    GenomicFeatures_1.20.4                     AnnotationDbi_1.30.1                      
[29] Biobase_2.28.0                             GenomicRanges_1.20.6                       GenomeInfoDb_1.4.2                         IRanges_2.2.7                             
[33] S4Vectors_0.6.5                            VennDiagram_1.6.16                         futile.logger_1.4.1                        RColorBrewer_1.1-2                        
[37] biomaRt_2.24.1                             BiocGenerics_0.14.0                        ggplot2_1.0.1                              reshape2_1.4.1                            
[41] gplots_2.17.0                              Rcpp_0.12.1                                apcluster_1.4.1                            mgcv_1.8-7                                
[45] nlme_3.1-122                              

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                 matrixStats_0.14.2           httr_1.0.0                   tools_3.2.2                  doRNG_1.6                    nor1mix_1.2-1               
 [7] R6_2.1.1                     KernSmooth_2.23-15           colorspace_1.2-6             base64_1.1                   preprocessCore_1.30.0        pkgmaker_0.22               
[13] caTools_1.17.1               scales_0.3.0                 genefilter_1.50.0            quadprog_1.5-5               stringr_1.0.0                digest_0.6.8                
[19] illuminaio_0.10.0            siggenes_1.42.0              GEOquery_2.34.0              htmltools_0.2.6              limma_3.24.15                BiocInstaller_1.18.4        
[25] shiny_0.12.2                 mclust_5.0.2                 BiocParallel_1.2.21          gtools_3.5.0                 RCurl_1.95-4.7               magrittr_1.5                
[31] Matrix_1.2-2                 munsell_0.4.2                proto_0.3-10                 stringi_0.5-5                MASS_7.3-44                  zlibbioc_1.14.0             
[37] plyr_1.8.3                   gdata_2.17.0                 splines_3.2.2                multtest_2.24.0              annotate_1.46.1              rngtools_1.2.4              
[43] codetools_0.2-14             futile.options_1.0.0         XML_3.98-1.3                 lambda.r_1.1.7               httpuv_1.3.3                 gtable_0.1.2                
[49] reshape_0.8.5                mime_0.4                     xtable_1.7-4                 survival_2.38-3              registry_0.3                 interactiveDisplayBase_1.6.1

Thank you for your help.

Best,

Rob

Wonderful, thank you. Please let me know if you encounter any difficulties in reproducing the behavior.

Hi Rob,

Thanks for reporting this. fiveUTRsByTranscript() and threeUTRsByTranscript() were both broken when the TxDb object had "user defined" seqlevels and/or a set of "active/inactive" seqlevels defined on it.

This is fixed in GenomicFeatures 1.20.6, which should become available via biocLite() on Thursday morning (Seattle time).

Cheers,

H.

Hi Hervé,

Thank you for looking into this. I'm looking forwards to the updated version of GenomicFeatures, and will let you know if I encounter any difficulties.

Best,

Rob