Exporting a GenomicRanges object as GTF/GFF file
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rubi ▴ 90
@rubi-6462
Last seen 3.1 years ago

Hi,

 

I'm trying to export a GenomicRanges object as a GTF file using rtrackleyr's export:

Here's an example GTF file downloaded from:

ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//gtf/bacteria_90_collection/_chrysanthemum_coronarium_phytoplasma/_chrysanthemum_coronarium_phytoplasma.ASM74406v1.32.gtf.gz

If I do:

library(rtracklayer)
library(GenomicRanges

export(import("_chrysanthemum_coronarium_phytoplasma.ASM74406v1.32.gtf.gz"),con="test.gtf")

I get this error:

Error in .subset2(instance, "x") : this S4 class is not subsettable

 

Any idea?

 

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Biostrings_2.42.1             XVector_0.14.0                Gviz_1.18.1                   setEnrichmentTests_0.0.0.9000 org.Ss.eg.db_3.4.0            org.Sc.sgd.db_3.4.0          
 [7] org.Rn.eg.db_3.4.0            org.Pt.eg.db_3.4.0            org.Mmu.eg.db_3.4.0           org.Mm.eg.db_3.4.0            org.Hs.eg.db_3.4.0            org.Cf.eg.db_3.4.0           
[13] org.Ce.eg.db_3.4.0            ggdendro_0.1-20               dendextend_1.5.2              fastcluster_1.1.22            cluster_2.0.5                 tidyr_0.6.3                  
[19] GOSemSim_2.0.1                matrixStats_0.51.0            doParallel_1.0.10             iterators_1.0.8               foreach_1.4.3                 snpEnrichment_1.7.0          
[25] piano_1.14.0                  topGO_2.26.0                  SparseM_1.72                  GO.db_3.4.0                   AnnotationDbi_1.36.0          Biobase_2.34.0               
[31] fgsea_1.0.2                   Rcpp_0.12.11.1                graph_1.50.0                  gageData_2.12.0               gage_2.24.0                   stringi_1.1.5                
[37] biomaRt_2.30.0                scales_0.4.1                  RColorBrewer_1.1-2            zoo_1.7-13                    gplots_3.0.1                  reshape2_1.4.2               
[43] plotrix_3.6-3                 Hmisc_3.17-4                  Formula_1.2-1                 survival_2.40-1               lattice_0.20-34               data.table_1.9.6             
[49] annotationData_0.1.0          dplyr_0.5.0                   plyr_1.8.4                    magrittr_1.5                  gtable_0.2.0                  gridExtra_2.2.1              
[55] plotly_4.7.0                  ggplot2_2.2.1.9000            rtracklayer_1.34.1            GenomicRanges_1.26.2          GenomeInfoDb_1.10.0           IRanges_2.8.1                
[61] S4Vectors_0.12.1              BiocGenerics_0.20.0           yaml_2.1.14                   doBy_4.5-15                  

loaded via a namespace (and not attached):
 [1] RSQLite_1.0.0                 htmlwidgets_0.8               trimcluster_0.1-2             BiocParallel_1.8.1            munsell_0.4.3                 codetools_0.2-15             
 [7] chron_2.3-47                  colorspace_1.3-2              BiocInstaller_1.24.0          robustbase_0.92-6             labeling_0.3                  slam_0.1-40                  
[13] biovizBase_1.22.0             sets_1.0-16                   diptest_0.75-7                R6_2.2.0                      flexmix_2.3-13                bitops_1.0-6                 
[19] assertthat_0.2.0              nnet_7.3-12                   ensembldb_1.6.2               rlang_0.1.1                   splines_3.3.2                 lazyeval_0.2.0               
[25] acepack_1.4.1                 dichromat_2.0-0               GenomicFeatures_1.26.0        snpStats_1.24.0               crosstalk_1.0.0               httpuv_1.3.3                 
[31] tools_3.3.2                   relations_0.6-6               zlibbioc_1.20.0               purrr_0.2.2.2                 RCurl_1.95-4.8                rpart_4.1-10                 
[37] viridis_0.4.0                 SummarizedExperiment_1.2.3    mvtnorm_1.0-5                 whisker_0.3-2                 mime_0.5                      xtable_1.8-2                 
[43] XML_3.98-1.4                  mclust_5.2                    tibble_1.3.3                  KernSmooth_2.23-15            htmltools_0.3.6               DBI_0.5-1                    
[49] MASS_7.3-45                   fpc_2.1-10                    Matrix_1.2-7.1                marray_1.52.0                 gdata_2.17.0                  igraph_1.0.1                 
[55] GenomicAlignments_1.8.4       foreign_0.8-67                annotate_1.52.0               VariantAnnotation_1.20.2      stringr_1.1.0                 digest_0.6.12                
[61] fastmatch_1.0-4               kernlab_0.9-25                shiny_1.0.2                   Rsamtools_1.26.1              gtools_3.5.0                  modeltools_0.2-21            
[67] jsonlite_1.4                  BSgenome_1.42.0               viridisLite_0.2.0             limma_3.30.2                  KEGGREST_1.14.0               httr_1.2.1                   
[73] DEoptimR_1.0-6                interactiveDisplayBase_1.12.0 png_0.1-7                     prabclus_2.2-6                class_7.3-14                  AnnotationHub_2.6.4          
[79] latticeExtra_0.6-28           caTools_1.17.1 

 

 

 

genomicranges rtracklayer gtf gff export • 889 views
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Please provide sessionInfo().

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Please upgrade your R/Bioconductor and let us know if you still get this error. It seems to work on my side.

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