modifications {EpiTxDb} | R Documentation

## Getting modification data from a `EpiTxDb-object`

### Description

`modifications` and `modificationsBy` are functions to extract modification annotation from a `EpiTxDb` object.

`modifiedSeqsByTranscript` returns a `ModRNAStringSet` from a `EpiTxDb` object and compatible `RNAStringSet` object. This used the `combineIntoModstrings()` function from the `Modstrings` package.

### Usage

    modifications(
      x,
      columns = c("mod_id", "mod_type", "mod_name"),
      filter = NULL,
      use.names = FALSE,
      ...
    )

    modificationsBy(
      x,
      by = c("seqnames", "mod_type", "reaction", "specifier", "specifier_type"),
      ...
    )

    modifiedSeqsByTranscript(x, sequences, ...)

    ## S4 method for signature 'EpiTxDb'
    modifications(
      x,
      columns = c("mod_id", "mod_type", "mod_name"),
      filter = NULL,
      use.names = FALSE
    )

    ## S4 method for signature 'EpiTxDb'
    modificationsBy(
      x,
      by = c("seqnames", "modtype", "reaction", "specifier", "specifiertype")
    )

    ## S4 method for signature 'EpiTxDb,DNAStringSet'
    modifiedSeqsByTranscript(x, sequences)

### Arguments

`x` | a `EpiTxDb`
`columns` | Columns to include in the result. If the vector is named, those names are used for the corresponding column in the element metadata of the returned object. (default: `columns = c("mod_id","mod_type","mod_name")`)
`filter` | Either NULL or a named list of vectors to be used to restrict the output. Valid names for this list are: "mod_id", "mod_type", "mod_name", "sn_id", "sn_name", "rx_genename", "rx_ensembl", "rx_ensembltrans", "rx_entrezid", "spec_genename", "spec_type", "spec_ensembl", "spec_ensembltrans", "spec_entrezid" , "ref_type" and "ref". (default: `filter = NULL`)
`use.names` | `TRUE` or `FALSE`. If `TRUE`, the modification names are set as the names of the returned object. (default: `use.names = FALSE`)
`...` | Not used.
`by` | By which information type should the result be split into? A `character` value from one of the following values: seqnames mod_type reaction specifier specifier_type
`sequences` | A `RNAStringSet`, which can be used as input for `combineIntoModstrings()`. See `?combineIntoModstrings` for additional details.

### Value

a `GRanges` object for `modifications` and a `GRangesList` for `modificationsBy`.

### Examples

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

[Package EpiTxDb version 1.0.0 Index]