ModInosine-functions {RNAmodR} | R Documentation

## Functions for ModInosine

### Description

All of the functions of `Modifier` and the `ModifierSet` classes are inherited by the `ModInosine` and `ModSetInosine` classes.

Check below for the specifically implemented functions.

### Usage

    ## S4 replacement method for signature 'ModInosine'
    settings(x) <- value

    ## S4 method for signature 'ModInosine'
    aggregateData(x)

    ## S4 method for signature 'ModInosine'
    findMod(x)

    ## S4 method for signature 'ModInosine'
    getDataTrack(x, name, type, ...)

    ## S4 method for signature 'ModInosine,GRanges'
    plotDataByCoord(x, coord, type = "score", window.size = 15L, ...)

    ## S4 method for signature 'ModInosine'
    plotData(x, name, from = 1L, to = 30L, type = "score", ...)

    ## S4 method for signature 'ModSetInosine,GRanges'
    plotDataByCoord(x, coord, type = "score", window.size = 15L, ...)

    ## S4 method for signature 'ModSetInosine'
    plotData(x, name, from = 1L, to = 30L, type = "score", ...)

### Arguments

`x` | a `Modifier` or a `ModifierSet` object. For more details see also the man pages for the functions mentioned below.
`value` | See `settings`
`coord, name, from, to, type, window.size, ...` | See `plotData`

### Details

`ModInosine` specific arguments for plotData:

- `colour.bases` - a named character vector of `length = 4` for the colours of the individual bases. The names are expected to be `c("G","A","U","C")`

### Value

- `settings` See `settings`.

- `aggregate` See `aggregate`.

- `modify` See `modify`.

- `getDataTrack` a list of `DataTrack` objects. See `plotDataByCoord`.

- `plotData` See `plotDataByCoord`.

- `plotDataByCoord` See `plotDataByCoord`.

### Examples

    data(msi,package="RNAmodR")
    mi <- msi[[1]]
    settings(mi)
    ## Not run:
    aggregate(mi)
    modify(mi)

    ## End(Not run)
    getDataTrack(mi, "1", mainScore(mi))

[Package RNAmodR version 1.4.2 Index]