pRoloc (version 1.12.4)

getPredictions: 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.

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)