Run bambu
Applying bambu to bamFiles
se <- bambu(reads = bamFiles, annotations = HsChr22BambuAnnotation, genome = genomeSequence)
bambu returns a SummarizedExperiment object
se
##> class: RangedSummarizedExperiment
##> dim: 1542 6
##> metadata(2): incompatibleCounts warnings
##> assays(4): counts CPM fullLengthCounts uniqueCounts
##> rownames(1542): BambuTx1 BambuTx2 ... ENST00000641933 ENST00000641967
##> rowData names(11): TXNAME GENEID ... txid eqClassById
##> colnames(6): 17c3bd19552d0f_3844 17c3bd7ee4641b_3846 ...
##> 17c3bd3686d5e7_3852 17c3bd6e8dd009_3854
##> colData names(1): name
Visualizing gene examples
We can visualize the annotated and novel isoforms identified in this
gene example using plot functions from bambu
plotBambu(se, type = "annotation", gene_id = "ENSG00000099968")
##> [[1]]
##> TableGrob (3 x 1) "arrange": 3 grobs
##> z cells name grob
##> 1 1 (2-2,1-1) arrange gtable[layout]
##> 2 2 (3-3,1-1) arrange gtable[layout]
##> 3 3 (1-1,1-1) arrange text[GRID.text.245]
sessionInfo()
##> R Under development (unstable) (2024-10-21 r87258)
##> Platform: x86_64-pc-linux-gnu
##> Running under: Ubuntu 24.04.1 LTS
##>
##> Matrix products: default
##> BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
##> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##>
##> locale:
##> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
##> [3] LC_TIME=en_GB LC_COLLATE=C
##> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
##> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
##> [9] LC_ADDRESS=C LC_TELEPHONE=C
##> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##>
##> time zone: America/New_York
##> tzcode source: system (glibc)
##>
##> attached base packages:
##> [1] stats4 stats graphics grDevices utils datasets methods
##> [8] base
##>
##> other attached packages:
##> [1] bambu_3.7.0
##> [2] SummarizedExperiment_1.35.5
##> [3] Biobase_2.65.1
##> [4] MatrixGenerics_1.17.1
##> [5] matrixStats_1.4.1
##> [6] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000
##> [7] BSgenome_1.73.1
##> [8] rtracklayer_1.65.0
##> [9] BiocIO_1.15.2
##> [10] ggbio_1.53.0
##> [11] ggplot2_3.5.1
##> [12] Rsamtools_2.21.2
##> [13] Biostrings_2.73.2
##> [14] XVector_0.45.0
##> [15] GenomicRanges_1.57.2
##> [16] GenomeInfoDb_1.41.2
##> [17] IRanges_2.39.2
##> [18] S4Vectors_0.43.2
##> [19] NanoporeRNASeq_1.15.0
##> [20] ExperimentHub_2.13.1
##> [21] AnnotationHub_3.13.3
##> [22] BiocFileCache_2.13.2
##> [23] dbplyr_2.5.0
##> [24] BiocGenerics_0.51.3
##>
##> loaded via a namespace (and not attached):
##> [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_1.8.9
##> [4] magrittr_2.0.3 GenomicFeatures_1.57.1 farver_2.1.2
##> [7] rmarkdown_2.28 zlibbioc_1.51.2 vctrs_0.6.5
##> [10] memoise_2.0.1 RCurl_1.98-1.16 base64enc_0.1-3
##> [13] progress_1.2.3 htmltools_0.5.8.1 S4Arrays_1.5.11
##> [16] curl_5.2.3 xgboost_1.7.8.1 SparseArray_1.5.45
##> [19] Formula_1.2-5 sass_0.4.9 bslib_0.8.0
##> [22] htmlwidgets_1.6.4 httr2_1.0.5 plyr_1.8.9
##> [25] cachem_1.1.0 GenomicAlignments_1.41.0 mime_0.12
##> [28] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-1
##> [31] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.13
##> [34] digest_0.6.37 colorspace_2.1-1 GGally_2.2.1
##> [37] AnnotationDbi_1.67.0 OrganismDbi_1.47.0 Hmisc_5.1-3
##> [40] RSQLite_2.3.7 labeling_0.4.3 filelock_1.0.3
##> [43] fansi_1.0.6 httr_1.4.7 abind_1.4-8
##> [46] compiler_4.5.0 bit64_4.5.2 withr_3.0.1
##> [49] htmlTable_2.4.3 backports_1.5.0 BiocParallel_1.39.0
##> [52] DBI_1.2.3 ggstats_0.7.0 highr_0.11
##> [55] biomaRt_2.61.3 rappdirs_0.3.3 DelayedArray_0.31.14
##> [58] rjson_0.2.23 tools_4.5.0 foreign_0.8-87
##> [61] nnet_7.3-19 glue_1.8.0 restfulr_0.0.15
##> [64] grid_4.5.0 checkmate_2.3.2 cluster_2.1.6
##> [67] reshape2_1.4.4 generics_0.1.3 gtable_0.3.6
##> [70] tidyr_1.3.1 ensembldb_2.29.1 hms_1.1.3
##> [73] data.table_1.16.2 xml2_1.3.6 utf8_1.2.4
##> [76] BiocVersion_3.20.0 pillar_1.9.0 stringr_1.5.1
##> [79] dplyr_1.1.4 lattice_0.22-6 bit_4.5.0
##> [82] biovizBase_1.53.0 RBGL_1.81.0 tidyselect_1.2.1
##> [85] knitr_1.48 gridExtra_2.3 ProtGenerics_1.37.1
##> [88] xfun_0.48 stringi_1.8.4 UCSC.utils_1.1.0
##> [91] lazyeval_0.2.2 yaml_2.3.10 evaluate_1.0.1
##> [94] codetools_0.2-20 tibble_3.2.1 graph_1.83.0
##> [97] BiocManager_1.30.25 cli_3.6.3 rpart_4.1.23
##> [100] munsell_0.5.1 jquerylib_0.1.4 dichromat_2.0-0.1
##> [103] Rcpp_1.0.13 png_0.1-8 XML_3.99-0.17
##> [106] parallel_4.5.0 blob_1.2.4 prettyunits_1.2.0
##> [109] AnnotationFilter_1.29.0 bitops_1.0-9 txdbmaker_1.1.2
##> [112] VariantAnnotation_1.51.2 scales_1.3.0 purrr_1.0.2
##> [115] crayon_1.5.3 rlang_1.1.4 KEGGREST_1.45.1
##> [118] formatR_1.14
