Extract marker/unknown subsets

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.

See also

sampleMSnSet testMSnSet and markers for markers encoding.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
mrk <- markerMSnSet(dunkley2006)
unk <- unknownMSnSet(dunkley2006)
dim(dunkley2006)
#> [1] 689  16
dim(mrk)
#> [1] 261  16
dim(unk)
#> [1] 428  16
table(fData(dunkley2006)$markers)
#> 
#>      ER lumen   ER membrane         Golgi Mitochondrion            PM 
#>            14            45            28            55            46 
#>       Plastid      Ribosome           TGN       unknown       vacuole 
#>            20            19            13           428            21 
table(fData(mrk)$markers)
#> 
#>      ER lumen   ER membrane         Golgi Mitochondrion            PM 
#>            14            45            28            55            46 
#>       Plastid      Ribosome           TGN       vacuole 
#>            20            19            13            21 
table(fData(unk)$markers)
#> 
#> unknown 
#>     428 
## matrix-encoded markers
dunkley2006 <- mrkVecToMat(dunkley2006)
dim(markerMSnSet(dunkley2006, "Markers"))
#> [1] 261  16
stopifnot(all.equal(featureNames(markerMSnSet(dunkley2006, "Markers")),
                    featureNames(markerMSnSet(dunkley2006, "markers"))))
dim(unknownMSnSet(dunkley2006, "Markers"))
#> [1] 428  16
stopifnot(all.equal(featureNames(unknownMSnSet(dunkley2006, "Markers")),
                    featureNames(unknownMSnSet(dunkley2006, "markers"))))