A unifying bioinformatics framework for spatial proteomics

Documentation for package ‘pRoloc’ version 1.8.0

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-- A --

-- C --

checkFeatureNamesOverlap	Check feature names overlap
checkFvarOverlap	Compare a feature variable overlap
chi2	The PCP 'chi square' method
chi2-method	The PCP 'chi square' method
chi2-methods	The PCP 'chi square' method
class:AnnotationParams	Class '"AnnotationParams"'
class:GenRegRes	Class '"GenRegRes"' and '"ThetaRegRes"'
class:ThetaRegRes	Class '"GenRegRes"' and '"ThetaRegRes"'
combineThetaRegRes	Class '"GenRegRes"' and '"ThetaRegRes"'

-- D --

Class '"AnnotationParams"'

-- E --

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

-- F --

f1Count	Class '"GenRegRes"' and '"ThetaRegRes"'
f1Count-method	Class '"GenRegRes"' and '"ThetaRegRes"'
favourPrimary	Class '"GenRegRes"' and '"ThetaRegRes"'
filterBinMSnSet	Filter a binary MSnSet
filterZeroCols	Remove 0 columns/rows
filterZeroRows	Remove 0 columns/rows

-- G --

GenRegRes	Class '"GenRegRes"' and '"ThetaRegRes"'
GenRegRes-class	Class '"GenRegRes"' and '"ThetaRegRes"'
getAnnotationParams	Class '"AnnotationParams"'
getF1Scores	Class '"GenRegRes"' and '"ThetaRegRes"'
getF1Scores-method	Class '"GenRegRes"' and '"ThetaRegRes"'
getGOEvidenceCodes	GO Evidence Codes
getGOFromFeatures	Retrieve GO terms for feature names
getMarkerClasses	Returns the organelle classes in an 'MSnSet'
getMarkers	Returns the organelle markers in an 'MSnSet'
getParams	Class '"GenRegRes"' and '"ThetaRegRes"'
getParams-method	Class '"GenRegRes"' and '"ThetaRegRes"'
getParams-method	Undocumented/unexported entries
getPredictions	Returns the predictions in an 'MSnSet'
getRegularisedParams	Class '"GenRegRes"' and '"ThetaRegRes"'
getRegularisedParams-method	Class '"GenRegRes"' and '"ThetaRegRes"'
getRegularizedParams	Class '"GenRegRes"' and '"ThetaRegRes"'
getRegularizedParams-method	Class '"GenRegRes"' and '"ThetaRegRes"'
getSeed	Class '"GenRegRes"' and '"ThetaRegRes"'
getSeed-method	Class '"GenRegRes"' and '"ThetaRegRes"'
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"' and '"ThetaRegRes"'
getWarnings-method	Class '"GenRegRes"' and '"ThetaRegRes"'

-- H --

Highlight features of interest on a plot2D figure

-- K --

knnClassification	knn classification
knnOptimisation	knn parameter optimisation
knnOptimization	knn parameter optimisation
knnPrediction	knn classification
knnRegularisation	knn parameter optimisation
knntlClassification	knn transfer learning classification
knntlOptimisation	theta parameter optimisation
ksvmClassification	ksvm classification
ksvmOptimisation	ksvm parameter optimisation
ksvmOptimization	ksvm parameter optimisation
ksvmPrediction	ksvm classification
ksvmRegularisation	ksvm parameter optimisation

-- L --

levelPlot	Class '"GenRegRes"' and '"ThetaRegRes"'
levelPlot-method	Class '"GenRegRes"' and '"ThetaRegRes"'
levelPlot-method	Undocumented/unexported entries
lopims	A complete LOPIMS pipeline
lopims1	A complete LOPIMS pipeline
lopims2	A complete LOPIMS pipeline
lopims3	A complete LOPIMS pipeline
lopims4	A complete LOPIMS pipeline
lopims5	A complete LOPIMS pipeline

-- M --

makeGoSet	Creates a GO feature 'MSnSet'
makeNaData	Create a data with missing values
makeNaData2	Create a data with missing values
markerMSnSet	Extract marker/unknown subsets
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

-- N --

nbClassification	nb classification
nbOptimisation	nb paramter optimisation
nbOptimization	nb paramter optimisation
nbPrediction	nb classification
nbRegularisation	nb paramter optimisation
nndist	Nearest neighbour distances
nndist-method	Nearest neighbour distances
nndist-methods	Nearest neighbour distances
nnetClassification	nnet classification
nnetOptimisation	nnet parameter optimisation
nnetOptimization	nnet parameter optimisation
nnetPrediction	nnet classification
nnetRegularisation	nnet parameter optimisation

-- P --

perTurboClassification	perTurbo classification
perTurboOptimisation	PerTurbo parameter optimisation
perTurboOptimization	PerTurbo parameter optimisation
phenoDisco	Runs the 'phenoDisco' algorithm.
plot-method	Class '"GenRegRes"' and '"ThetaRegRes"'
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

-- R --

-- S --

sampleMSnSet	Extract a stratified sample of an 'MSnSet'
setAnnotationParams	Class '"AnnotationParams"'
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 '"AnnotationParams"'
show-method	Class '"GenRegRes"' and '"ThetaRegRes"'
show-method	Undocumented/unexported entries
showGOEvidenceCodes	GO Evidence Codes
svmClassification	svm classification
svmOptimisation	svm parameter optimisation
svmOptimization	svm parameter optimisation
svmPrediction	svm classification
svmRegularisation	svm parameter optimisation

-- T --

testMarkers	Tests marker class sizes
testMSnSet	Create a stratified 'test' 'MSnSet'
ThetaRegRes	Class '"GenRegRes"' and '"ThetaRegRes"'
ThetaRegRes-class	Class '"GenRegRes"' and '"ThetaRegRes"'
thetas	Draw matrix of thetas to test

-- U --

undocumented	Undocumented/unexported entries
unknownMSnSet	Extract marker/unknown subsets

-- W --

Create a data with missing values