To create an EpiTxDb object a number of different
functions are available. The most univeral functions are
makeEpiTxDb and makeEpiTxDbFromGRanges.
makeEpiTxDb uses four data.frames as input,
whereas makeEpiTxDbFromGRanges is a wrapper for information
available as a GRanges object.
The other functions are makeEpiTxDbFromRMBase and
makeEpiTxDbFromtRNAdb, which are aimed to make data
available from the RMBase v2.0 database (Xuan et al. 2017; Sun et al. 2015) or the
tRNAdb (Jühling et al.
2009; Sprinzl and Vassilenko 2005). However, before creating
your EpiTxDb objects, have a look at the already available
resources for H. sapiens, M. musculus and
S. cerevisiae.
Additional metadata can be provided as separate
data.frame for all functions. The data.frame
must have two columns name and value.
## Warning: replacing previous import 'GenomicFeatures::makeTxDbPackage' by
## 'txdbmaker::makeTxDbPackage' when loading 'EpiTxDb'## Warning: replacing previous import
## 'GenomicFeatures::supportedUCSCFeatureDbTables' by
## 'txdbmaker::supportedUCSCFeatureDbTables' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGFF' by
## 'txdbmaker::makeTxDbFromGFF' when loading 'EpiTxDb'## Warning: replacing previous import
## 'GenomicFeatures::makeTxDbPackageFromBiomart' by
## 'txdbmaker::makeTxDbPackageFromBiomart' when loading 'EpiTxDb'## Warning: replacing previous import
## 'GenomicFeatures::supportedMiRBaseBuildValues' by
## 'txdbmaker::supportedMiRBaseBuildValues' when loading 'EpiTxDb'## Warning: replacing previous import
## 'GenomicFeatures::supportedUCSCFeatureDbTracks' by
## 'txdbmaker::supportedUCSCFeatureDbTracks' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::browseUCSCtrack' by
## 'txdbmaker::browseUCSCtrack' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::getChromInfoFromBiomart'
## by 'txdbmaker::getChromInfoFromBiomart' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDbFromGRanges' by
## 'txdbmaker::makeTxDbFromGRanges' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::supportedUCSCtables' by
## 'txdbmaker::supportedUCSCtables' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDbFromBiomart' by
## 'txdbmaker::makeTxDbFromBiomart' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::UCSCFeatureDbTableSchema'
## by 'txdbmaker::UCSCFeatureDbTableSchema' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDbFromEnsembl' by
## 'txdbmaker::makeTxDbFromEnsembl' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDb' by
## 'txdbmaker::makeTxDb' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeFDbPackageFromUCSC' by
## 'txdbmaker::makeFDbPackageFromUCSC' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDbFromUCSC' by
## 'txdbmaker::makeTxDbFromUCSC' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeTxDbPackageFromUCSC'
## by 'txdbmaker::makeTxDbPackageFromUCSC' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makePackageName' by
## 'txdbmaker::makePackageName' when loading 'EpiTxDb'## Warning: replacing previous import 'GenomicFeatures::makeFeatureDbFromUCSC' by
## 'txdbmaker::makeFeatureDbFromUCSC' when loading 'EpiTxDb'makeEpiTxDb and
makeEpiTxDbFromGRangesThe creation of an etdb object is quite easy starting with a
GRanges object.
gr <- GRanges(seqnames = "test",
ranges = IRanges::IRanges(1,1),
strand = "+",
DataFrame(mod_id = 1L,
mod_type = "Am",
mod_name = "Am_1"))
etdb <- makeEpiTxDbFromGRanges(gr, metadata = data.frame(name = "test",
value = "Yes"))## Creating EpiTxDb object ... done## EpiTxDb object:
## # Db type: EpiTxDb
## # Supporting package: EpiTxDb
## # test: Yes
## # Nb of modifications: 1
## # Db created by: EpiTxDb package from Bioconductor
## # Creation time: 2024-10-30 07:20:03 +0000 (Wed, 30 Oct 2024)
## # EpiTxDb version at creation time: 1.19.0
## # RSQLite version at creation time: 2.3.7
## # DBSCHEMAVERSION: 1.0## name value
## 1 Db type EpiTxDb
## 2 Supporting package EpiTxDb
## 3 test Yes
## 4 Nb of modifications 1
## 5 Db created by EpiTxDb package from Bioconductor
## 6 Creation time 2024-10-30 07:20:03 +0000 (Wed, 30 Oct 2024)
## 7 EpiTxDb version at creation time 1.19.0
## 8 RSQLite version at creation time 2.3.7
## 9 DBSCHEMAVERSION 1.0Additional data can be provided via the metadata columns of the
GRanges object. For supported columns have a look at
?makeEpiTxDb or ?makeEpiTxDbFromGRanges.
makeEpiTxDbFromtRNAdbThe information of the tRNAdb can be accessed via the
tRNAdbImport package using the RNA database. As a result a
ModRNAStringSet object is returned from which the
modifications can be extracted using separate().
The only input require is a valid organism name returned by
listAvailableOrganismsFromtRNAdb().
# Currently not run since the server is not available
etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae")
etdbFor additional information have a look at
?makeEpiTxDbFromtRNAdb. The result returned from the tRNAdb
is also available as GRanges object, if
gettRNAdbDataAsGRanges() is used.
makeEpiTxDbFromRMBaseAnalogous to the example above makeEpiTxDbFromRMBase()
will download the data from the RMBase v2.0. Three inputs are required,
organism, genome and modtype,
which have to valid bia the functions
listAvailableOrganismsFromRMBase(),
.listAvailableGenomesFromRMBase() and
listAvailableModFromRMBase.
Internally, the files are cached using the BiocFileCache
package and passed to makeEpiTxDbFromRMBaseFiles(), which
can also be used with locally stored files. The resuls for creating the
EpiTxDb class are processed from these files via the
getRMBaseDataAsGRanges() function.
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] EpiTxDb_1.19.0 Modstrings_1.21.0 Biostrings_2.75.0
## [4] XVector_0.45.0 AnnotationDbi_1.69.0 Biobase_2.67.0
## [7] GenomicRanges_1.57.2 GenomeInfoDb_1.41.2 IRanges_2.39.2
## [10] S4Vectors_0.43.2 BiocGenerics_0.53.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] tRNAdbImport_1.23.0 tidyselect_1.2.1
## [3] dplyr_1.1.4 blob_1.2.4
## [5] filelock_1.0.3 bitops_1.0-9
## [7] fastmap_1.2.0 RCurl_1.98-1.16
## [9] BiocFileCache_2.15.0 GenomicAlignments_1.41.0
## [11] rex_1.2.1 XML_3.99-0.17
## [13] digest_0.6.37 lifecycle_1.0.4
## [15] KEGGREST_1.45.1 RSQLite_2.3.7
## [17] magrittr_2.0.3 compiler_4.4.1
## [19] rlang_1.1.4 sass_0.4.9
## [21] progress_1.2.3 tools_4.4.1
## [23] utf8_1.2.4 yaml_2.3.10
## [25] rtracklayer_1.65.0 knitr_1.48
## [27] prettyunits_1.2.0 S4Arrays_1.5.11
## [29] bit_4.5.0 curl_5.2.3
## [31] DelayedArray_0.31.14 xml2_1.3.6
## [33] abind_1.4-8 BiocParallel_1.41.0
## [35] txdbmaker_1.1.2 sys_3.4.3
## [37] grid_4.4.1 fansi_1.0.6
## [39] colorspace_2.1-1 ggplot2_3.5.1
## [41] scales_1.3.0 biomaRt_2.63.0
## [43] SummarizedExperiment_1.35.5 cli_3.6.3
## [45] rmarkdown_2.28 crayon_1.5.3
## [47] generics_0.1.3 httr_1.4.7
## [49] rjson_0.2.23 DBI_1.2.3
## [51] cachem_1.1.0 stringr_1.5.1
## [53] zlibbioc_1.51.2 parallel_4.4.1
## [55] BiocManager_1.30.25 restfulr_0.0.15
## [57] matrixStats_1.4.1 vctrs_0.6.5
## [59] Matrix_1.7-1 jsonlite_1.8.9
## [61] hms_1.1.3 bit64_4.5.2
## [63] GenomicFeatures_1.57.1 maketools_1.3.1
## [65] jquerylib_0.1.4 glue_1.8.0
## [67] codetools_0.2-20 gtable_0.3.6
## [69] stringi_1.8.4 BiocIO_1.17.0
## [71] UCSC.utils_1.1.0 munsell_0.5.1
## [73] tibble_3.2.1 pillar_1.9.0
## [75] rappdirs_0.3.3 htmltools_0.5.8.1
## [77] GenomeInfoDbData_1.2.13 R6_2.5.1
## [79] dbplyr_2.5.0 httr2_1.0.5
## [81] evaluate_1.0.1 lattice_0.22-6
## [83] png_0.1-8 Rsamtools_2.21.2
## [85] memoise_2.0.1 bslib_0.8.0
## [87] Structstrings_1.21.0 tRNA_1.23.0
## [89] SparseArray_1.5.45 xfun_0.48
## [91] MatrixGenerics_1.17.1 buildtools_1.0.0
## [93] pkgconfig_2.0.3