ModAlkAnilineSeq-functions {RNAmodR.AlkAnilineSeq} | R Documentation

## Functions for ModAlkAnilineSeq

### Description

All of the functions of `Modifier` and the `ModifierSet` classes are inherited by the `ModAlkAnilineSeq` and `ModSetAlkAnilineSeq` classes.

### Usage

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

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

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

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

    ## S4 method for signature 'ModAlkAnilineSeq,GRanges'
    plotDataByCoord(
      x,
      coord,
      type = c("ends", "scoreNC", "scoreSR"),
      window.size = 15L,
      ...
    )

    ## S4 method for signature 'ModAlkAnilineSeq'
    plotData(
      x,
      name,
      from = 1L,
      to = 30L,
      type = c("ends", "scoreNC", "scoreSR"),
      ...
    )

    ## S4 method for signature 'ModSetAlkAnilineSeq,GRanges'
    plotDataByCoord(
      x,
      coord,
      type = c("scoreNC", "scoreSR", "ends"),
      window.size = 15L,
      ...
    )

    ## S4 method for signature 'ModSetAlkAnilineSeq'
    plotData(
      x,
      name,
      from = 1L,
      to = 30L,
      type = c("scoreNC", "scoreSR", "ends"),
      ...
    )

### 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

`ModAlkAnilineSeq` specific arguments for plotData:

- `colour` - a named character vector of `length = 4` for the colours of the individual histograms. The names are expected to be `c("scoreNC","scoreSR")`

### Value

- `settings` See `settings`.

- `aggregate` See `aggregate`.

- `modify` See `modify`.

- `getDataTrack` a list of `DataTrack` object.

- `plotData` See `plotDataByCoord`.

- `plotDataByCoord` See `plotDataByCoord`.

### Examples

    data(msaas,package="RNAmodR.AlkAnilineSeq")
    maas <- msaas[[1]]
    settings(maas)
    aggregate(maas)
    modify(maas)
    getDataTrack(maas, "1", mainScore(maas))

[Package RNAmodR.AlkAnilineSeq version 1.2.0 Index]