EpiTxDb-class {EpiTxDb}R Documentation

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

See Also

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

[Package EpiTxDb version 1.2.1 Index]