testMarkers: Tests marker class sizes

In lgatto/pRoloc: A unifying bioinformatics framework for spatial proteomics

Tests marker class sizes

Description

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.

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.

Value

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

Author(s)

Laurent Gatto

See Also

getMarkers and minMarkers

Examples

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

lgatto/pRoloc documentation built on Oct. 23, 2024, 12:51 a.m.