getPredictions: Returns the predictions in an 'MSnSet'

In pRoloc: A unifying bioinformatics framework for spatial proteomics

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)

pRoloc documentation built on Nov. 8, 2020, 6:26 p.m.