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rubi
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@rubi-6462
Last seen 6.3 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
Please provide sessionInfo().
Please upgrade your R/Bioconductor and let us know if you still get this error. It seems to work on my side.