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.
getMarkers(object, fcol = "markers", names = TRUE, verbose = TRUE)An instance of class "MSnSet".
The name of the markers column in the featureData
slot. Default is "markers".
A logical indicating if the markers vector should
be named. Ignored if markers are encoded as a matrix.
If TRUE, a marker table is printed and the markers
are returned invisibly. If FALSE, the markers are returned.
A character (matrix) of length (ncol)
ncol(object), depending on the vector or matrix encoding of
the markers.
See getMarkerClasses to get the classes
only. See markers for details about spatial markers
storage and encoding.
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