setMLModel<- {RNAmodR.ML} | R Documentation

## The ModifierML class

### Description

The `ModifierML` class is a virtual class, which provides the central functionality for searching with a machine learning models for patterns of post-transcriptional RNA modifications in high throughput sequencing data.

It extends the virtual `Modifier` class form the `RNAmodR` package and add the `useMLModel` function. If not called directly for a `ModifierML` class, the `useMLModel` will be called from the `aggregate` function.

The slot `mlModel` is added and serves a dual purpose. If `mlModel` is a character, a class of the type `ModifierMLModel` is created upon creation of a `ModifierML` object. However, for developing purposes the slot can also remain empty and a `ModifierMLModel` object can be set using the `setMLModel` function and retrieved using the `getMLModel`. If the `mlModel` slot is empty, the `findMod` setting will be set to `FALSE` and the `ModifierML` object will be returned just with the aggregate data. Such an object can then be used to train a machine learning model. The data can be accessed using `trainingData`.

### Usage

    setMLModel(x) <- value

    getMLModel(x)

    hasMLModel(x)

    useMLModel(x)

    ## S4 replacement method for signature 'ModifierML'
    setMLModel(x) <- value

    ## S4 method for signature 'ModifierML'
    getMLModel(x)

    ## S4 method for signature 'ModifierML'
    hasMLModel(x)

    ## S4 method for signature 'ModifierML'
    aggregate(x, force = FALSE)

    ## S4 method for signature 'ModifierML'
    useMLModel(x)

    ## S4 method for signature 'ModifierML'
    modify(x, force = FALSE)

### Arguments

`x` | a `ModifierML` object.
`value` | a `ModifierMLModel` object
`force` | whether to recreate the aggregated data, if it is already stored inside the `Modifier` object.

### Value

a `ModifierML` object

### Slots

`mlModel`

  a `character` describing a class name for creating a `ModifierMLModel` object or a `ModifierMLModel` object itself. If `mlModel` is a `character`, the class will tried to be create by calling a function of the same name.

### See Also

`Modifier`

### Examples

    # an example implementation of a ModifierML object
    setClass("ModMLExample",
             contains = c("RNAModifierML"),
             prototype = list(mod = c("D"),
                              score = "score",
                              dataType = c("PileupSequenceData",
                                           "CoverageSequenceData"),
                              mlModel = character(0)))
    # constructor function for ModMLExample
    ModMLExample <- function(x, annotation = NA, sequences = NA, seqinfo = NA,
                             ...){
      RNAmodR:::Modifier("ModMLExample", x = x, annotation = annotation,
                         sequences = sequences, seqinfo = seqinfo, ...)
    }

[Package RNAmodR.ML version 1.0.0 Index]