makeEpiTxDbFromtRNAdb {EpiTxDb} | R Documentation

## Create a `EpiTxDb` object from tRNAdb resources

### Description

`makeEpiTxDbFromtRNAdb` will make use of the tRNAdb online resources and extract the modification information from the RNA database.

If a named `DNAStringSet` is provided as `sequences`, the result from the tRNAdb will be matched against the sequences. Valid matches will be used as transcript identifiers and returned after a check of modification compatibility with the provided sequence. By this process multiple copies of transcripts can be associated with a single modification.

`makeEpiTxDbFromtRNAdb` uses the functions provided by the `tRNAdbImport` package. `import.tRNAdb` will be used with `database = "RNA"` and the three different values for `origin`.

### Usage

    gettRNAdbDataAsGRanges(
      organism,
      sequences = NULL,
      dbURL = tRNAdbImport::TRNA_DB_URL
    )

    makeEpiTxDbFromtRNAdb(
      organism,
      sequences = NULL,
      metadata = NULL,
      dbURL = tRNAdbImport::TRNA_DB_URL
    )

    listAvailableOrganismsFromtRNAdb()

### Arguments

`organism` | A `character` value for an organism available on the tRNAdb website.
`sequences` | A named `DNAStringSet` or `RNAStringSet`, which will be used to associate a tRNAdb result with a specific transcript.
`dbURL` | The URL to the tRNA db website.
`metadata` | See `makeEpiTxDb`

### Value

a `EpiTxDb` object.

### References

Juehling F, Moerl M, Hartmann RK, Sprinzl M, Stadler PF, Puetz J. 2009. "tRNAdb 2009: compilation of tRNA sequences and tRNA genes." Nucleic Acids Research, Volume 37 (suppl_1): D159–162. doi:10.1093/nar/gkn772.

### Examples

    ## Not run:
    # getting just the annotation data
    etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae")

    # For associating the result with transcripts, provide and additional
    # named DNAStringSet object. Matching will be done against each sequence
    # allowing 5 mismatches and indels. The final result will be checked for
    # validity regarding the identity of the modifications
    etdb <- makeEpiTxDbFromtRNAdb("Saccharomyces cerevisiae",
                                  some_transcript_sequences)

    ## End(Not run)

[Package EpiTxDb version 1.4.0 Index]