This function creates a stratified 'test' MSnSet which can be used
for algorihtmic development. A "MSnSet" containing only
the marker proteins, as defined in fcol, is returned with a new
feature data column appended called test in which a stratified subset
of these markers has been relabelled as 'unknowns'.
Arguments
- object
An instance of class
"MSnSet"- fcol
The feature meta-data column name containing the marker definitions on which the data will be stratified. Default is
markers.- size
The size of the data set to be extracted. Default is 0.2 (20 percent).
- seed
The optional random number generator seed.
Value
An instance of class "MSnSet" which
contains only the proteins that have a labelled localisation
i.e. the marker proteins, as defined in fcol and a new
column in the feature data slot called test which has part
of the labels relabelled as "unknown" class (the number of
proteins renamed as "unknown" is according to the parameter size).
Examples
library(pRolocdata)
data(tan2009r1)
sample <- testMSnSet(tan2009r1)
getMarkers(sample, "test")
#> organelleMarkers
#> Cytoskeleton ER Golgi Lysosome Nucleus
#> 5 22 10 6 16
#> PM Peroxisome Proteasome Ribosome 40S Ribosome 60S
#> 27 3 12 16 25
#> mitochondrion unknown
#> 23 46
all(dim(sample) == dim(markerMSnSet(tan2009r1)))
#> [1] TRUE