Get the organelle markers in an MSnSet

Convenience accessor to the organelle markers in an MSnSet. This function returns the organelle markers of an MSnSet instance. As a side effect, it print out a marker table.

Usage

getMarkers(object, fcol = "markers", names = TRUE, verbose = TRUE)

Arguments

object

An instance of class "MSnSet".

fcol

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

names

A logical indicating if the markers vector should be named. Ignored if markers are encoded as a matrix.

verbose

If TRUE, a marker table is printed and the markers are returned invisibly. If FALSE, the markers are returned.

Value

A character (matrix) of length (ncol) ncol(object), depending on the vector or matrix encoding of the markers.

See also

See getMarkerClasses to get the classes only. See markers for details about spatial markers storage and encoding.

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
## marker vectors
myVmarkers <- getMarkers(dunkley2006)
#> organelleMarkers
#>      ER lumen   ER membrane         Golgi Mitochondrion            PM 
#>            14            45            28            55            46 
#>       Plastid      Ribosome           TGN       unknown       vacuole 
#>            20            19            13           428            21 
head(myVmarkers)
#>  AT1G09210  AT1G21750  AT1G51760  AT1G56340  AT2G32920  AT2G47470 
#> "ER lumen" "ER lumen" "ER lumen" "ER lumen" "ER lumen" "ER lumen" 
## marker matrix
dunkley2006 <- mrkVecToMat(dunkley2006, mfcol = "Markers")
myMmarkers <- getMarkers(dunkley2006, fcol = "Markers")
#> Localisation count:
#>   0   1 
#> 428 261 
#> Single localisations:
#>      ER lumen   ER membrane         Golgi Mitochondrion            PM 
#>            14            45            28            55            46 
#>       Plastid      Ribosome           TGN       vacuole 
#>            20            19            13            21 
#> Multiple localisations:
#>   none
head(myMmarkers)
#>           ER lumen ER membrane Golgi Mitochondrion PM Plastid Ribosome TGN
#> AT1G09210        1           0     0             0  0       0        0   0
#> AT1G21750        1           0     0             0  0       0        0   0
#> AT1G51760        1           0     0             0  0       0        0   0
#> AT1G56340        1           0     0             0  0       0        0   0
#> AT2G32920        1           0     0             0  0       0        0   0
#> AT2G47470        1           0     0             0  0       0        0   0
#>           vacuole
#> AT1G09210       0
#> AT1G21750       0
#> AT1G51760       0
#> AT1G56340       0
#> AT2G32920       0
#> AT2G47470       0