pRoloc (version 1.12.4)

getMarkerClasses: Returns the organelle classes in an 'MSnSet'

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", verbose = TRUE, ...)

Arguments

object

An instance of class "MSnSet".

fcol

The name of the markers column in the featureData slot. Default is markers.

verbose

If TRUE, a character vector of the organelle classes is printed and the classes are returned invisibly. If FALSE, the markers are returned.

...

Additional parameters passed to sort from the base package.

Value

A character vector of the organelle classes in the data.

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))