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

- `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

[Package EpiTxDb version 1.2.1 Index]