testMarkers: Tests marker class sizes
In pRoloc: A unifying bioinformatics framework for spatial proteomics

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1 2	testMarkers(object, xval = 5, n = 2, fcol = "markers", error = FALSE)

`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.

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.

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

Laurent Gatto

getMarkers and minMarkers

library("pRolocdata")
data(dunkley2006)
getMarkers(dunkley2006)
testMarkers(dunkley2006)
toosmall <- testMarkers(dunkley2006, xval = 15)
toosmall
try(testMarkers(dunkley2006, xval = 15, error = TRUE))