# A unifying bioinformatics framework for spatial proteomics

## Documentation for package ‘pRoloc’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H K L M N P R S T U W

## -- A --

addLegend | Adds a legend
addLegend_v1 | Adds a legend
addMarkers | Adds markers to the data
andy2011params | Class '"AnnotationParams"'
AnnotationParams | Class '"AnnotationParams"'
AnnotationParams-class | Class '"AnnotationParams"'

## -- 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 --

dunkley2006params | 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 --

highlightOnPlot | 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 --

rfClassification | rf classification
rfOptimisation | svm parameter optimisation
rfOptimization | svm parameter optimisation
rfPrediction | rf classification
rfRegularisation | svm parameter optimisation

## -- 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 --

whichNA | Create a data with missing values