stianlagstad
commented
4 years ago Thanks again @ziadbakouny18 ! This should be fixed in the release version 1.12.2 and the devel version 1.13.1 - as soon as BioConductor builds the new versions. Please verify that it works as you expect.
Hello Stian,
I am trying to run your plot_fusion_transcript_with_protein_domain without a BAM file but I am getting an error. These are the code and data I am using:
4) edb <- EnsDb.Hsapiens.v86 fusions<- import_soapfuse(tcga_annot_soapfuse_format_unique.txt, "hg38")
plot_fusion_transcript_with_protein_domain( fusion = get_fusion_by_id(fusions, 14), edb = edb, bedfile = full_enst_to_pfam_map_format.txt", gene_upstream_transcript = "ENST00000377604", gene_downstream_transcript = "ENST00000315869", plot_downstream_protein_domains_if_fusion_is_out_of_frame = TRUE)
And this is the error I am getting: Error in file.exists(bamfile) : invalid 'file' argument
Is there not a way to do run this if I do not want to plot the coverage on the plot?
1) sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.2 EnsDb.Hsapiens.v86_2.99.0 chimeraviz_1.12.0
[6] ensembldb_2.10.2 AnnotationFilter_1.10.0 GenomicFeatures_1.38.0 Gviz_1.30.0 biomaRt_2.42.0
[11] dendsort_0.3.3 metaseqR_1.26.0 qvalue_2.18.0 limma_3.42.0 DESeq_1.38.0
[16] locfit_1.5-9.1 EDASeq_2.20.0 ShortRead_1.44.1 GenomicAlignments_1.22.1 SummarizedExperiment_1.16.1 [21] DelayedArray_0.12.1 matrixStats_0.55.0 Rsamtools_2.2.1 GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
[26] Biostrings_2.54.0 XVector_0.26.0 BiocParallel_1.20.1 reshape2_1.4.3 Hmisc_4.3-0
[31] Formula_1.2-3 lattice_0.20-38 viridis_0.5.1 viridisLite_0.3.0 RColorBrewer_1.1-2
[36] pheatmap_1.0.12 psych_1.9.12 survminer_0.4.6 ggpubr_0.2.4 magrittr_1.5
[41] survival_3.1-8 table1_1.1 msigdbr_7.0.1 GSVA_1.34.0 GSEABase_1.48.0
[46] graph_1.64.0 annotate_1.64.0 XML_3.98-1.20 AnnotationDbi_1.48.0 IRanges_2.20.1
[51] S4Vectors_0.24.1 Biobase_2.46.0 BiocGenerics_0.32.0 broom_0.5.3 ggrepel_0.8.1
[56] gmodels_2.18.1 BH_1.72.0-2 data.table_1.12.8 forcats_0.4.0 stringr_1.4.0
[61] purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3 ggplot2_3.2.1
[66] tidyverse_1.3.0 dplyr_0.8.3
loaded via a namespace (and not attached): [1] rappdirs_0.3.1 rtracklayer_1.46.0 R.methodsS3_1.7.1 acepack_1.4.1
[5] bit64_0.9-7 knitr_1.26 aroma.light_3.16.0 R.utils_2.9.2
[9] rpart_4.1-15 hwriter_1.3.2 RCurl_1.95-4.12 generics_0.0.2
[13] org.Mm.eg.db_3.10.0 preprocessCore_1.48.0 RSQLite_2.1.5 bit_1.1-14
[17] BiocStyle_2.14.2 xml2_1.2.2 lubridate_1.7.4 httpuv_1.5.2
[21] assertthat_0.2.1 xfun_0.11 hms_0.5.2 evaluate_0.14
[25] promises_1.1.0 fansi_0.4.0 progress_1.2.2 caTools_1.17.1.3
[29] readxl_1.3.1 Rgraphviz_2.30.0 km.ci_0.5-2 DBI_1.1.0
[33] geneplotter_1.64.0 htmlwidgets_1.5.1 corrplot_0.84 backports_1.1.5
[37] vctrs_0.2.1 abind_1.4-5 log4r_0.3.1 withr_2.1.2
[41] BSgenome_1.54.0 checkmate_1.9.4 prettyunits_1.0.2 mnormt_1.5-5
[45] cluster_2.1.0 NBPSeq_0.3.0 lazyeval_0.2.2 crayon_1.3.4
[49] genefilter_1.68.0 edgeR_3.28.0 pkgconfig_2.0.3 nlme_3.1-143
[53] ProtGenerics_1.18.0 nnet_7.3-12 rlang_0.4.2 lifecycle_0.1.0
[57] affyio_1.56.0 modelr_0.1.5 dichromat_2.0-0 cellranger_1.1.0
[61] Matrix_1.2-18 KMsurv_0.1-5 zoo_1.8-6 reprex_0.3.0
[65] base64enc_0.1-3 png_0.1-7 rjson_0.2.20 bitops_1.0-6
[69] NOISeq_2.30.0 R.oo_1.23.0 KernSmooth_2.23-16 blob_1.2.0
[73] brew_1.0-6 jpeg_0.1-8.1 ggsignif_0.6.0 scales_1.1.0
[77] memoise_1.1.0 plyr_1.8.5 gplots_3.0.1.1 gdata_2.18.0
[81] zlibbioc_1.32.0 compiler_3.6.1 ArgumentCheck_0.10.2 cli_2.0.0
[85] affy_1.64.0 htmlTable_1.13.3 MASS_7.3-51.5 tidyselect_0.2.5
[89] vsn_3.54.0 stringi_1.4.3 yaml_2.2.0 askpass_1.1
[93] latticeExtra_0.6-29 survMisc_0.5.5 VariantAnnotation_1.32.0 tools_3.6.1
[97] rstudioapi_0.10 foreign_0.8-74 gridExtra_2.3 digest_0.6.23
[101] BiocManager_1.30.10 shiny_1.4.0 Rcpp_1.0.3 BiocVersion_3.10.1
[105] later_1.0.0 org.Hs.eg.db_3.10.0 httr_1.4.1 RCircos_1.2.1
[109] biovizBase_1.34.1 colorspace_1.4-1 rvest_0.3.5 fs_1.3.1
[113] splines_3.6.1 shinythemes_1.1.2 xtable_1.8-4 jsonlite_1.6
[117] baySeq_2.20.0 zeallot_0.1.0 R6_2.4.1 pillar_1.4.3
[121] htmltools_0.4.0 mime_0.8 glue_1.3.1 fastmap_1.0.1
[125] DT_0.11 interactiveDisplayBase_1.24.0 utf8_1.1.4 curl_4.3
[129] gtools_3.8.1 openssl_1.4.1 rmarkdown_2.0 munsell_0.5.0
[133] GenomeInfoDbData_1.2.2 haven_2.2.0 gtable_0.3.0
2) Fusion caller: I am using some custom fusions derived from a multi-caller that I have reformatted to a soapfuse format.
3) OS: Windows 10