pRoloc (version 1.12.4)

orgQuants: 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.

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)