EpiTxDb: creating an EpiTxDb object

In EpiTxDb: Storing and accessing epitranscriptomic information using the AnnotationDbi interface

BiocStyle::markdown(css.files = c('custom.css'))

Introduction

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.2017;@Sun.2015] or the tRNAdb [@Juehling.2009;@Sprinzl.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.

suppressPackageStartupMessages({
    library(GenomicRanges)
    library(EpiTxDb)
})

library(GenomicRanges)
library(EpiTxDb)

makeEpiTxDb and makeEpiTxDbFromGRanges

The 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"))
etdb
metadata(etdb)

Additional data can be provided via the metadata columns of the GRanges object. For supported columns have a look at ?makeEpiTxDb or ?makeEpiTxDbFromGRanges.

makeEpiTxDbFromtRNAdb

The 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().

etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae")
etdb

For additional information have a look at ?makeEpiTxDbFromtRNAdb. The result returned from the tRNAdb is also available as GRanges object, if gettRNAdbDataAsGRanges() is used.

makeEpiTxDbFromRMBase

Analogous 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.

etdb <- makeEpiTxDbFromRMBase(organism = "Saccharomyces cerevisiae",
                              genome = "sacCer3",
                              modtype = "m1A")

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.

Session info

sessionInfo()

References

EpiTxDb documentation built on March 26, 2021, 6 p.m.