getMarkerClasses: Returns the organelle classes in an 'MSnSet'

In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description

Convenience accessor to the organelle classes in an 'MSnSet'. This function returns the organelle classes of an MSnSet instance. As a side effect, it prints out the classes.

Usage

getMarkerClasses(object, fcol = "markers", ...)

Arguments

object	An instance of class "MSnSet".
fcol	The name of the markers column in the featureData slot. Default is markers.
...	Additional parameters passed to sort from the base package.

Value

A character vector of the organelle classes in the data.

Author(s)

Lisa Breckels and Laurent Gatto

See Also

getMarkers to extract the marker proteins. See markers for details about spatial markers storage and encoding.

Examples

library("pRolocdata")
data(dunkley2006)
organelles <- getMarkerClasses(dunkley2006)
## same if markers encoded as a matrix
dunkley2006 <- mrkVecToMat(dunkley2006, mfcol = "Markers")
organelles2 <- getMarkerClasses(dunkley2006, fcol = "Markers")
stopifnot(all.equal(organelles, organelles2))

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