orgQuants: Returns organelle-specific quantile scores

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

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)

lgatto/pRoloc documentation built on Nov. 27, 2024, 12:14 a.m.