orgQuants: Returns organelle-specific quantile scores
In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description Usage Arguments Value Author(s) See Also Examples

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

1	orgQuants(object, fcol, scol, mcol = "markers", t, verbose = TRUE)

`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.

A named vector of organelle thresholds.

Lisa Breckels

getPredictions to get organelle predictions based on calculated thresholds.

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)