EpiTxDb.Sc.sacCer3 0.99.3
EpiTxDb.Sc.sacCer3 contains post-transcriptional RNA modifications from RMBase
v2.0 (Xuan et al. 2017) and tRNAdb (Jühling et al. 2009) and
can be accessed through the functions EpiTxDb.Sc.sacCer3.tRNAdb() and
EpiTxDb.Sc.sacCer3.RMBase()
library(EpiTxDb.Sc.sacCer3)etdb <- EpiTxDb.Sc.sacCer3.tRNAdb()## snapshotDate(): 2020-03-31## downloading 1 resources## retrieving 1 resource## loading from cacheetdb## EpiTxDb object:
## # Db type: EpiTxDb
## # Supporting package: EpiTxDb
## # Data source: tRNAdb
## # Organism: Saccharomyces cerevisiae
## # Genome: sacCer3
## # Coordinates: per Transcript
## # Nb of modifications: 2990
## # Db created by: EpiTxDb package from Bioconductor
## # Creation time: 2020-02-26 10:43:09 +0100 (Wed, 26 Feb 2020)
## # EpiTxDb version at creation time: 0.99.0
## # RSQLite version at creation time: 2.2.0
## # DBSCHEMAVERSION: 1.0Modification information can be accessed through the typical function for an
EpiTxDb object, for example modifications():
modifications(etdb)## GRanges object with 2990 ranges and 3 metadata columns:
## seqnames ranges strand | mod_id mod_type
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] tA(AGC)D_tRNA 9 + | 1 m1G
## [2] tA(AGC)F_tRNA 9 + | 2 m1G
## [3] tA(AGC)G_tRNA 9 + | 3 m1G
## [4] tA(AGC)H_tRNA 9 + | 4 m1G
## [5] tA(AGC)J_tRNA 9 + | 5 m1G
## ... ... ... ... . ... ...
## [2986] tY(GUA)Q_tRNA 29 + | 3860 m2G
## [2987] tY(GUA)Q_tRNA 30 + | 3861 Y
## [2988] tY(GUA)Q_tRNA 40 + | 3862 i6A
## [2989] tY(GUA)Q_tRNA 66 + | 3863 m5U
## [2990] tY(GUA)Q_tRNA 67 + | 3864 Y
## mod_name
## <character>
## [1] m1G_9_tA(AGC)D_tRNA
## [2] m1G_9_tA(AGC)F_tRNA
## [3] m1G_9_tA(AGC)G_tRNA
## [4] m1G_9_tA(AGC)H_tRNA
## [5] m1G_9_tA(AGC)J_tRNA
## ... ...
## [2986] m2G_29_tY(GUA)Q_tRNA
## [2987] Y_30_tY(GUA)Q_tRNA
## [2988] i6A_40_tY(GUA)Q_tRNA
## [2989] m5U_66_tY(GUA)Q_tRNA
## [2990] Y_67_tY(GUA)Q_tRNA
## -------
## seqinfo: 258 sequences from sacCer3 genome; no seqlengthsFor a more detailed overview and explanation of the functionality of the
EpiTxDb class, have a look at the EpiTxDb package.
sessionInfo()## R Under development (unstable) (2020-04-01 r78128)
## Platform: x86_64-apple-darwin17.7.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
##
## Matrix products: default
## BLAS: /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] EpiTxDb.Sc.sacCer3_0.99.3 EpiTxDb_0.99.5
## [3] Modstrings_1.3.12 Biostrings_2.55.7
## [5] XVector_0.27.2 AnnotationDbi_1.49.1
## [7] IRanges_2.21.8 S4Vectors_0.25.14
## [9] Biobase_2.47.3 AnnotationHub_2.19.9
## [11] BiocFileCache_1.11.4 dbplyr_1.4.2
## [13] BiocGenerics_0.33.3 BiocStyle_2.15.6
##
## loaded via a namespace (and not attached):
## [1] matrixStats_0.56.0 bitops_1.0-6
## [3] assertive.models_0.0-2 bit64_0.9-7
## [5] progress_1.2.2 httr_1.4.1
## [7] GenomeInfoDb_1.23.16 assertive.datetimes_0.0-2
## [9] tools_4.1.0 R6_2.4.1
## [11] colorspace_1.4-1 DBI_1.1.0
## [13] assertive.data_0.0-3 assertive.reflection_0.0-4
## [15] tidyselect_1.0.0 prettyunits_1.1.1
## [17] bit_1.1-15.2 curl_4.3
## [19] compiler_4.1.0 cli_2.0.2
## [21] assertive.properties_0.0-4 xml2_1.3.0
## [23] DelayedArray_0.13.8 rtracklayer_1.47.0
## [25] assertive.files_0.0-2 bookdown_0.18
## [27] scales_1.1.0 tRNA_1.5.2
## [29] askpass_1.1 rappdirs_0.3.1
## [31] stringr_1.4.0 digest_0.6.25
## [33] Rsamtools_2.3.7 rmarkdown_2.1
## [35] assertive.numbers_0.0-2 pkgconfig_2.0.3
## [37] htmltools_0.4.0 fastmap_1.0.1
## [39] rlang_0.4.5 RSQLite_2.2.0
## [41] assertive_0.3-5 shiny_1.4.0.2
## [43] BiocParallel_1.21.2 dplyr_0.8.5
## [45] RCurl_1.98-1.1 magrittr_1.5
## [47] GenomeInfoDbData_1.2.2 Matrix_1.2-18
## [49] munsell_0.5.0 Rcpp_1.0.4
## [51] fansi_0.4.1 lifecycle_0.2.0
## [53] stringi_1.4.6 assertive.base_0.0-7
## [55] yaml_2.2.1 SummarizedExperiment_1.17.5
## [57] zlibbioc_1.33.1 grid_4.1.0
## [59] blob_1.2.1 promises_1.1.0
## [61] crayon_1.3.4 lattice_0.20-41
## [63] tRNAdbImport_1.5.6 assertive.code_0.0-3
## [65] GenomicFeatures_1.39.7 hms_0.5.3
## [67] knitr_1.28 pillar_1.4.3
## [69] GenomicRanges_1.39.3 assertive.sets_0.0-3
## [71] codetools_0.2-16 biomaRt_2.43.4
## [73] XML_3.99-0.3 glue_1.3.2
## [75] BiocVersion_3.11.1 Structstrings_1.3.5
## [77] evaluate_0.14 BiocManager_1.30.10
## [79] vctrs_0.2.4 httpuv_1.5.2
## [81] gtable_0.3.0 openssl_1.4.1
## [83] purrr_0.3.3 assertive.strings_0.0-3
## [85] assertthat_0.2.1 ggplot2_3.3.0
## [87] xfun_0.12 mime_0.9
## [89] xtable_1.8-4 assertive.types_0.0-3
## [91] later_1.0.0 assertive.data.uk_0.0-2
## [93] tibble_3.0.0 GenomicAlignments_1.23.2
## [95] memoise_1.1.0 assertive.matrices_0.0-2
## [97] ellipsis_0.3.0 assertive.data.us_0.0-2
## [99] interactiveDisplayBase_1.25.0Jühling, Frank, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, and Joern Pütz. 2009. “TRNAdb 2009: Compilation of tRNA Sequences and tRNA Genes.” Nucleic Acids Research 37: D159–D162. https://doi.org/10.1093/nar/gkn772.
Xuan, Jia-Jia, Wen-Ju Sun, Peng-Hui Lin, Ke-Ren Zhou, Shun Liu, Ling-Ling Zheng, Liang-Hu Qu, and Jian-Hua Yang. 2017. “RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.” Nucleic Acids Research 46 (D1): D327–D334. https://doi.org/10.1093/nar/gkx934.