Modifier-functions {RNAmodR} | R Documentation

## Modifier/ModifierSet functions

### Description

For the `Modifier` and `ModifierSet` classes a number of functions are implemented to access the data stored by the object.

The `validAggregate` and `validModification` functions check if `settings` have been modified, after the data was loaded. This potentially invalidates them. To update the data, run the `aggregate` or the `modify` function.

### Usage

    bamfiles(x)

    mainScore(x)

    modifierType(x)

    modType(x)

    dataType(x)

    sequenceData(x)

    sequences(x, ...)

    validAggregate(x)

    validModification(x)

    ## S4 method for signature 'Modifier'
    show(object)

    ## S4 method for signature 'Modifier'
    bamfiles(x)

    ## S4 method for signature 'Modifier'
    conditions(object)

    ## S4 method for signature 'Modifier'
    mainScore(x)

    ## S4 method for signature 'Modifier'
    modifierType(x)

    ## S4 method for signature 'Modifier'
    modType(x)

    ## S4 method for signature 'Modifier'
    dataType(x)

    ## S4 method for signature 'Modifier'
    names(x)

    ## S4 method for signature 'Modifier'
    ranges(x)

    ## S4 method for signature 'Modifier'
    replicates(x)

    ## S4 method for signature 'Modifier'
    seqinfo(x)

    ## S4 method for signature 'Modifier'
    seqtype(x)

    ## S4 method for signature 'Modifier'
    sequenceData(x)

    ## S4 method for signature 'Modifier'
    sequences(x, modified = FALSE)

    ## S4 method for signature 'Modifier'
    validAggregate(x)

    ## S4 method for signature 'Modifier'
    validModification(x)

    ## S4 method for signature 'ModifierSet'
    show(object)

    ## S4 method for signature 'ModifierSet'
    bamfiles(x)

    ## S4 method for signature 'ModifierSet'
    conditions(object)

    ## S4 method for signature 'ModifierSet'
    mainScore(x)

    ## S4 method for signature 'ModifierSet'
    modifications(x, perTranscript = FALSE)

    ## S4 method for signature 'ModifierSet'
    modifierType(x)

    ## S4 method for signature 'ModifierSet'
    modType(x)

    ## S4 method for signature 'ModifierSet'
    dataType(x)

    ## S4 method for signature 'ModifierSet'
    ranges(x)

    ## S4 method for signature 'ModifierSet'
    replicates(x)

    ## S4 method for signature 'ModifierSet'
    seqinfo(x)

    ## S4 method for signature 'ModifierSet'
    seqtype(x)

    ## S4 method for signature 'ModifierSet'
    sequences(x, modified = FALSE)

### Arguments

`x, object` | a `Modifier` or `ModifierSet` class
`...` | Additional arguments.
`modified` | For `sequences`: `TRUE` or `FALSE`: Should the sequences be returned as a `ModRNAString`/`ModDNAString` with the found modifications added on top of the `RNAString`/ `DNAString`? See `combineIntoModstrings`.
`perTranscript` | `TRUE` or `FALSE`: Should the positions shown per transcript? (default: `perTranscript = FALSE`)

### Value

- `modifierType`: a character vector with the appropriate class Name of a `Modifier`.

- `modType`: a character vector with the modifications detected by the `Modifier` class.

- `seqtype`: a single character value defining if either "RNA" or "DNA" modifications are detected by the `Modifier` class.

- `mainScore`: a character vector.

- `sequenceData`: a `SequenceData` object.

- `modifications`: a `GRanges` or `GRangesList` object describing the found modifications.

- `seqinfo`: a `Seqinfo` object.

- `sequences`: a `RNAStingSet` object.

- `ranges`: a `GRangesList` object with each element per transcript.

- `bamfiles`: a `BamFileList` object.

- `validAggregate`: `TRUE` or `FALSE`. Checks if current settings are the same for which the data was aggregate

- `validModification`: `TRUE` or `FALSE`. Checks if current settings are the same for which modification were found

### See Also

`settings`

### Examples

    data(msi,package="RNAmodR")
    mi <- msi[[1]]
    modifierType(mi) # The class name of the Modifier object
    modifierType(msi)
    seqtype(mi)
    modType(mi)
    mainScore(mi)
    sequenceData(mi)
    modifications(mi)
    # general accessors
    seqinfo(mi)
    sequences(mi)
    ranges(mi)
    bamfiles(mi)

[Package RNAmodR version 1.2.3 Index]