ResultSet {MultiDataSet} | R Documentation

## Class ResultSet

### Description

Class `ResultSet` used to encapsulate results from `MEAL` and `omicrexposome`.

### Usage

    ## S4 method for signature 'ResultSet'
    fData(object)

    ## S4 method for signature 'ResultSet'
    getAssociation(object, rid = 1, coef = 2,
      contrast = NULL, fNames = NULL, ...)

    ## S4 method for signature 'ResultSet'
    length(x)

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

    ## S4 method for signature 'ResultSet'
    opt(object)

    ## S4 method for signature 'ResultSet,ANY'
    plot(x, y, rid = 1, coef = 2, contrast = NULL,
      type, tFC = 2, tPV = -log10(0.001), show.labels = TRUE,
      show.effect = FALSE, show.lambda = TRUE, fNames = c("chromosome",
      "start"), subset, highlight, ...)

    ## S4 method for signature 'ResultSet'
    varLabels(object)

    create_resultset(fOrigin, lResults, fData, lOptions = list())

### Arguments

`object` | A `ResultSet` object.
`rid` | Name or index of the internal result to be used
`coef` | Coefficient to be returne, usually 2
`contrast` | Numeric matrix with the contrasts used to perform the analyses
`fNames` | Character vector with the names of the fData columns that will be added to the results data.frame.
`...` | Further arguments passed to topTable
`x` | A `ResultSet` object.
`y` | -
`type` | Type of plot to be drawn
`tFC` | Threshold for log FC of effect
`tPV` | Threshold for P-Value
`show.labels` | (default `TRUE`) If set to `TRUE`, features are labelled.
`show.effect` | (default: `TRUE`). Used in volcano plot. If `TRUE`, effect is shown as FC instead of logFC.
`show.lambda` | (default: `TRUE`) If `TRUE` shows lambda score for the given model.
`subset` | GenomicRanges used to zoom a region in Manhattan plot
`highlight` | GenomicRanges used to highlight a region in Manhattan plot
`fOrigin` | Chracter with the function used to run the analysis.
`lResults` | List with the results
`fData` | List with the feature data.
`lOptions` | List with additional options

### Value

An object of class `ResultSet`

### Methods (by generic)

- `fData`: Returns `data.frame` with feature's data.

- `getAssociation`: Getter to obtain the raw `data.frame` from association and integration analysis.

- `length`: Returns the amoung of analyses stored in the `ResultSet`.

- `names`: Returns the names of the omics data used to create the `ResultSet`.

- `opt`: Returns a list with the options used to create the `ResultSet`

- `plot`: Allows to plot a series of plots (QQ plot, Manhattan plot and Volcano plot) depending on the results stored in the `ResultSet`.

- `varLabels`: Returns the names of the variables of the models used in a `ResultSet`.

### Slots

`fun_origin`

  Character containing the function that creates the object.

`results`

  List containing the results of the association/integration.

`fData`

  List containing the feature-data of the original objects.

`options`

  list of options used to create the `ResultSet`.

### Examples

    create_resultset("hello", list(), list(), list())

[Package MultiDataSet version 1.14.0 Index]