getPredictions {pRoloc} | R Documentation

## Returns the predictions in an 'MSnSet'

### Description

Convenience accessor to the predicted feature localisation in an 'MSnSet'. This function returns the predictions of an `MSnSet` instance. As a side effect, it prints out a prediction table.

### Usage

    getPredictions(object, fcol, scol, mcol = "markers", t = 0,
      verbose = TRUE)

### Arguments

`object` | An instance of class `"MSnSet"`.
`fcol` | The name of the prediction column in the `featureData` slot.
`scol` | The name of the prediction score column in the `featureData` slot. If missing, created by pasting '.scores' after `fcol`.
`mcol` | The feature meta data column containing the labelled training data.
`t` | The score threshold. Predictions with score < t are set to 'unknown'. Default is 0. It is also possible to define thresholds for each prediction class, in which case, `t` is a named numeric with names exactly matching the unique prediction class names.
`verbose` | If `TRUE`, a prediction table is printed and the predictions are returned invisibly. If `FALSE`, the predictions are returned.

### Value

An instance of class "MSnSet" with `fcol.pred` feature variable storing the prediction results according to the chosen threshold.

### Author(s)

Laurent Gatto and Lisa Breckels

### See Also

`orgQuants` for calculating organelle-specific thresholds.

### Examples

    library("pRolocdata")
    data(dunkley2006)
    res <- svmClassification(dunkley2006, fcol = "pd.markers",
                             sigma = 0.1, cost = 0.5)
    fData(res)$svm[500:510]
    fData(res)$svm.scores[500:510]
    getPredictions(res, fcol = "svm", t = 0) ## all predictions
    getPredictions(res, fcol = "svm", t = .9) ## single threshold
    ## 50% top predictions per class
    ts <- orgQuants(res, fcol = "svm", t = .5)
    getPredictions(res, fcol = "svm", t = ts)

[Package pRoloc version 1.22.2 Index]