addLegend | Adds a legend |
addLegend_v1 | Adds a legend |
addMarkers | Adds markers to the data |
chi2 | The PCP 'chi square' method |
chi2-method | The PCP 'chi square' method |
chi2-methods | The PCP 'chi square' method |
class:GenRegRes | Class '"GenRegRes"' |
empPvalues | Estimate empirical p-values for Chi^2 protein correlations. |
exprsToRatios | Calculate all ratio pairs |
exprsToRatios-method | Calculate all ratio pairs |
exprsToRatios-methods | Calculate all ratio pairs |
f1Count | Class '"GenRegRes"' |
f1Count-method | Class '"GenRegRes"' |
GenRegRes | Class '"GenRegRes"' |
GenRegRes-class | Class '"GenRegRes"' |
getF1Scores | Class '"GenRegRes"' |
getF1Scores-method | Class '"GenRegRes"' |
getMarkers | Returns the organelle markers in an 'MSnSet' |
getParams | Class '"GenRegRes"' |
getParams-method | Class '"GenRegRes"' |
getParams-method | Undocumented/unexported entries |
getPredictions | Returns the predictions in an 'MSnSet' |
getRegularisedParams | Class '"GenRegRes"' |
getRegularisedParams-method | Class '"GenRegRes"' |
getRegularizedParams | Class '"GenRegRes"' |
getRegularizedParams-method | Class '"GenRegRes"' |
getSeed | Class '"GenRegRes"' |
getSeed-method | Class '"GenRegRes"' |
getStockcol | Manage default colours and point characters |
getStockpch | Manage default colours and point characters |
getUnknowncol | Manage default colours and point characters |
getUnknownpch | Manage default colours and point characters |
getWarnings | Class '"GenRegRes"' |
getWarnings-method | Class '"GenRegRes"' |
knnClassification | knn classification |
knnOptimisation | knn parameter optimisation |
knnOptimization | knn parameter optimisation |
knnPrediction | knn classification |
knnRegularisation | knn parameter optimisation |
ksvmClassification | ksvm classification |
ksvmOptimisation | ksvm parameter optimisation |
ksvmOptimization | ksvm parameter optimisation |
ksvmPrediction | ksvm classification |
ksvmRegularisation | ksvm parameter optimisation |
levelPlot | Class '"GenRegRes"' |
levelPlot-method | Class '"GenRegRes"' |
levelPlot-method | Undocumented/unexported entries |
lopims | A complete LOPIMS pipeline |
makeNaData | Create a data with missing values |
makeNaData2 | Create a data with missing values |
markerSet | Extract marker subset |
minClassScore | Updates classes based on prediction scores |
minMarkers | Creates a reduced marker variable |
MLearn-method | The 'MLearn' interface for machine learning |
MLearnMSnSet | The 'MLearn' interface for machine learning |
MSnSetMLean | The 'MLearn' interface for machine learning |
nbClassification | nb classification |
nbOptimisation | nb paramter optimisation |
nbOptimization | nb paramter optimisation |
nbPrediction | nb classification |
nbRegularisation | nb paramter optimisation |
nnetClassification | nnet classification |
nnetOptimisation | nnet parameter optimisation |
nnetOptimization | nnet parameter optimisation |
nnetPrediction | nnet classification |
nnetRegularisation | nnet parameter optimisation |
perTurboClassification | perTurbo classification |
perTurboOptimisation | PerTurbo parameter optimisation |
perTurboOptimization | PerTurbo parameter optimisation |
phenoDisco | Runs the 'phenoDisco' algorithm. |
plot-method | Class '"GenRegRes"' |
plot-method | Undocumented/unexported entries |
plot2D | Plot organelle assignment data and results. |
plot2D_v1 | Plot organelle assignment data and results. |
plotDist | Plots the distribution of features across fractions |
plsdaClassification | plsda classification |
plsdaOptimisation | plsda parameter optimisation |
plsdaOptimization | plsda parameter optimisation |
plsdaPrediction | plsda classification |
plsdaRegularisation | plsda parameter optimisation |
pRolocmarkers | Organelle markers |
rfClassification | rf classification |
rfOptimisation | svm parameter optimisation |
rfOptimization | svm parameter optimisation |
rfPrediction | rf classification |
rfRegularisation | svm parameter optimisation |
setStockcol | Manage default colours and point characters |
setStockpch | Manage default colours and point characters |
setUnknowncol | Manage default colours and point characters |
setUnknownpch | Manage default colours and point characters |
show-method | Class '"GenRegRes"' |
show-method | Undocumented/unexported entries |
svmClassification | ksvm classification |
svmOptimisation | svm parameter optimisation |
svmOptimization | svm parameter optimisation |
svmPrediction | ksvm classification |
svmRegularisation | svm parameter optimisation |
testMarkers | Tests marker class sizes |
undocumented | Undocumented/unexported entries |
unknownSet | Extract marker subset |
whichNA | Create a data with missing values |