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Question: threeUTRsByTranscript appears to not work after invoking setter seqlevelsStyle
0
gravatar for Robert K. Bradley
2.2 years ago by
United States
Robert K. Bradley40 wrote:

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

ADD COMMENTlink modified 2.1 years ago • written 2.2 years ago by Robert K. Bradley40

Hi Rob,

Sorry for the late answer. I'm looking into this. Will let you know when it's fixed.

Thanks,

H.

ADD REPLYlink written 2.1 years ago by Hervé Pagès ♦♦ 13k
0
gravatar for Robert K. Bradley
2.1 years ago by
United States
Robert K. Bradley40 wrote:

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

ADD COMMENTlink written 2.1 years ago by Robert K. Bradley40
0
gravatar for Hervé Pagès
2.1 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Hervé Pagès ♦♦ 13k
0
gravatar for Robert K. Bradley
2.1 years ago by
United States
Robert K. Bradley40 wrote:

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

ADD COMMENTlink written 2.1 years ago by Robert K. Bradley40
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