orgQuants {pRoloc} | R Documentation

## Returns organelle-specific quantile scores

### Description

This function produces organelle-specific quantiles corresponding to the given classification scores.

### Usage

    orgQuants(object, fcol, scol, mcol = "markers", t, 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 name of the column containing the training data in the `featureData` slot. Default is `markers`.
`t` | The quantile threshold.
`verbose` | If `TRUE`, the calculated threholds are printed.

### Value

A named `vector` of organelle thresholds.

### Author(s)

Lisa Breckels

### See Also

`getPredictions` to get organelle predictions based on calculated thresholds.

### Examples

    library("pRolocdata")
    data(dunkley2006)
    res <- svmClassification(dunkley2006, fcol = "pd.markers",
                             sigma = 0.1, cost = 0.5)
    ## 50% top predictions per class
    ts <- orgQuants(res, fcol = "svm", t = .5)
    getPredictions(res, fcol = "svm", t = ts)

[Package pRoloc version 1.26.0 Index]