Calculates class weights to be used for parameter optimisation and
classification such as svmOptimisation or
svmClassification - see the pRoloc tutorial
vignette for an example. The weights are calculated for all
non-unknown classes the inverse of the number of
observations.
classWeights(object, fcol = "markers")An instance of class MSnSet
The name of the features to be weighted
A table of class weights
library("pRolocdata")
data(hyperLOPIT2015)
classWeights(hyperLOPIT2015)
#>
#> 40S Ribosome 60S Ribosome
#> 0.037037037 0.023255814
#> Actin cytoskeleton Cytosol
#> 0.076923077 0.023255814
#> Endoplasmic reticulum/Golgi apparatus Endosome
#> 0.009345794 0.076923077
#> Extracellular matrix Lysosome
#> 0.076923077 0.030303030
#> Mitochondrion Nucleus - Chromatin
#> 0.002610966 0.015625000
#> Nucleus - Non-chromatin Peroxisome
#> 0.011764706 0.058823529
#> Plasma membrane Proteasome
#> 0.019607843 0.029411765
data(dunkley2006)
classWeights(dunkley2006)
#>
#> ER lumen ER membrane Golgi Mitochondrion PM
#> 0.07142857 0.02222222 0.03571429 0.01818182 0.02173913
#> Plastid Ribosome TGN vacuole
#> 0.05000000 0.05263158 0.07692308 0.04761905