EpiTxDb-class: EpiTxDb objects

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

EpiTxDb objects

Description

The EpiTxDb class is a AnnotationDb type container for storing Epitranscriptomic information.

The information are typically stored on a per transcript and not as genomic coordinates, but the EpiTxDb class is agnostic to this. In case of genomic coordinates transcriptsBy will return modifications per chromosome.

Usage

## S4 method for signature 'EpiTxDb'
organism(object)

## S4 method for signature 'EpiTxDb'
seqinfo(x)

## S4 method for signature 'EpiTxDb'
seqlevels(x)

## S4 method for signature 'EpiTxDb'
as.list(x)

Arguments

x, object

a EpiTxDb object

Value

For

• organism() and seqlevels() a character vector

• seqinfo() a Seqinfo object

• as.list() a list

See Also

• makeEpiTxDbFromGRanges for creating a EpiTxDb object from a GRanges object and it's metadata columns

• makeEpiTxDbFromRMBase for creating a EpiTxDb object from RMBase online resources

• makeEpiTxDbFromtRNAdb for creating a EpiTxDb object from tRNAdb online resources

• makeEpiTxDb for creating a EpiTxDb object from data.frames

• modifications, modificationsBy for getting epitranscriptomic modification locations

• select for using the default interface of AnnotationDb objects.

• shiftGenomicToTranscript and shiftTranscriptToGenomic for transfering genomic to transcript coordinates and back again.

Examples

etdb_file <- system.file("extdata", "EpiTxDb.Hs.hg38.snoRNAdb.sqlite",
                        package="EpiTxDb")
etdb <- loadDb(etdb_file)
etdb

# general methods
seqinfo(etdb) #
seqlevels(etdb) # easy access to all transcript names

FelixErnst/EpiTxDb documentation built on March 31, 2024, 1:21 a.m.