markerMSnSet: Extract marker/unknown subsets

In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description

These function extract the marker or unknown proteins into a new MSnSet.

Usage

markerMSnSet(object, fcol = "markers")

unknownMSnSet(object, fcol = "markers")

Arguments

object	An instance of class MSnSet
fcol	The name of the feature data column, that will be used to separate the markers from the proteins of unknown localisation. When the markers are encoded as vectors, features of unknown localisation are defined as fData(object)[, fcol] == "unknown". For matrix-encoded markers, unlabelled proteins are defined as rowSums(fData(object)[, fcol]) == 0. Default is "markers".

Value

An new MSnSet with marker/unknown proteins only.

Author(s)

Laurent Gatto

See Also

sampleMSnSet testMSnSet and markers for markers encoding.

Examples

library("pRolocdata")
data(dunkley2006)
mrk <- markerMSnSet(dunkley2006)
unk <- unknownMSnSet(dunkley2006)
dim(dunkley2006)
dim(mrk)
dim(unk)
table(fData(dunkley2006)$markers)
table(fData(mrk)$markers)
table(fData(unk)$markers)
## matrix-encoded markers
dunkley2006 <- mrkVecToMat(dunkley2006)
dim(markerMSnSet(dunkley2006, "Markers"))
stopifnot(all.equal(featureNames(markerMSnSet(dunkley2006, "Markers")),
                    featureNames(markerMSnSet(dunkley2006, "markers"))))
dim(unknownMSnSet(dunkley2006, "Markers"))
stopifnot(all.equal(featureNames(unknownMSnSet(dunkley2006, "Markers")),
                    featureNames(unknownMSnSet(dunkley2006, "markers"))))

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