Tests marker class sizes

Tests if the marker class sizes are large enough for the parameter optimisation scheme, i.e. the size is greater that xval + n, where the default xval is 5 and n is 2. If the test is unsuccessful, a warning is thrown.

Usage

testMarkers(object, xval = 5, n = 2, fcol = "markers", error = FALSE)

Arguments

object

An instance of class "MSnSet".

xval

The number cross-validation partitions. See the xval argument in the parameter optimisation function(s). Default is 5.

n

Number of additional examples.

fcol

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

error

A logical specifying if an error should be thown, instead of a warning.

Value

If successfull, the test invisibly returns NULL. Else, it invisibly returns the names of the classes that have too few examples.

Details

In case the test indicates that a class contains too few examples, it is advised to either add some or, if not possible, to remove the class altogether (see minMarkers) as the parameter optimisation is likely to fail or, at least, produce unreliable results for that class.

See also

getMarkers and minMarkers

Author

Laurent Gatto

Examples

library("pRolocdata")
data(dunkley2006)
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 
testMarkers(dunkley2006)
toosmall <- testMarkers(dunkley2006, xval = 15)
#> Warning: ER lumen, TGN have/has less than 17 markers.
toosmall
#> [1] "ER lumen" "TGN"     
try(testMarkers(dunkley2006, xval = 15, error = TRUE))
#> Error in testMarkers(dunkley2006, xval = 15, error = TRUE) : 
#>   ER lumen, TGN have/has less than 17 markers.