makeEpiTxDbFromRMBase {EpiTxDb} | R Documentation

## Create a `EpiTxDb` object from RMBase v2.0 online resources

### Description

`makeEpiTxDbFromRMBase` will make use of the RMBase v2.0 online resources.

### Usage

    EPITXDB_RMBASE_URL

    downloadRMBaseFiles(organism, genome, modtype)

    makeEpiTxDbFromRMBase(
      organism,
      genome,
      modtype,
      tx = NULL,
      sequences = NULL,
      metadata = NULL,
      reassign.ids = FALSE
    )

    getRMBaseDataAsGRanges(files)

    makeEpiTxDbFromRMBaseFiles(
      files,
      tx = NULL,
      sequences = NULL,
      metadata = NULL,
      reassign.ids = FALSE
    )

    listAvailableOrganismsFromRMBase()

    listAvailableGenomesFromRMBase(organism)

    listAvailableModFromRMBase(organism, genome)

### Arguments

`organism` | A `character` value, which must match an organism descriptor on the RMBase download website.
`genome` | A `character` value, which must match a genome descriptor on the RMBase download website.
`modtype` | A `character` value, which must match one or more modification descriptors on the RMBase download website.
`tx` | A `GRangesList` object which will be used to shift the genomic coordinates to transcript coordinates. This is optional, but highly recommended. (default: `tx = NULL`).
`sequences` | A named `DNAStringSet` or `RNAStringSet`, which will be used to check whether the defined modifications are compatible with the original base. This uses `removeIncompatibleModifications()` function from the `Modstrings` package.
`metadata, reassign.ids` | See `makeEpiTxDb`
`files` | From `organism`, `genome` and `modtype` the available files will be downloaded using the `BiocFileCache` interface and passed on to `makeEpiTxDbFromRMBaseFiles`. However, individual files can be provided as well.

### Format

An object of class `character` of length 1.

### Value

a `EpiTxDb` object.

[Package EpiTxDb version 1.2.1 Index]