A unifying bioinformatics framework for spatial proteomics

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Documentation for package ‘pRoloc’ version 1.0.1

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addLegend 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"'
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"'
makeNaData Create a data with missing values
makeNaData2 Create a data with missing values
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"'
plot2D 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
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"'
svmClassification ksvm classification
svmOptimisation svm parameter optimisation
svmOptimization svm parameter optimisation
svmPrediction ksvm classification
svmRegularisation svm parameter optimisation
whichNA Create a data with missing values