A unifying bioinformatics framework for spatial proteomics


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Documentation for package ‘pRoloc’ version 1.10.0

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

pRoloc-package A unifying bioinformatics framework for spatial proteomics

-- A --

addLegend 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:SpatProtVis Class 'SpatProtVis'
class:ThetaRegRes Class '"GenRegRes"' and '"ThetaRegRes"'
col1 Draw 2 data sets on one PCA plot
col2 Draw 2 data sets on one PCA plot
combineThetaRegRes Class '"GenRegRes"' and '"ThetaRegRes"'

-- D --

data1 Draw 2 data sets on one PCA plot
data2 Draw 2 data sets on one PCA plot
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
flipGoTermId Convert GO ids to/from terms

-- 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
getLisacol Manage default colours and point characters
getMarkerClasses Returns the organelle classes in an 'MSnSet'
getMarkers Get 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"'
goIdToTerm Convert GO ids to/from terms
goTermToId Convert GO ids to/from terms

-- H --

highlightOnPlot Highlight features of interest on a plot2D figure

-- I --

isMrkMat Create a marker vector or matrix.
isMrkVec Create a marker vector or matrix.

-- 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
markers Create a marker vector or matrix.
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
move2Ds Displays a spatial proteomics animation
mrkEncoding Create a marker vector or matrix.
mrkMatAndVec Create a marker vector or matrix.
mrkMatToVec Create a marker vector or matrix.
mrkVecToMat Create a marker vector or matrix.
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 Class 'SpatProtVis'
plot-method Undocumented/unexported entries
plot2D Plot organelle assignment data and results.
plot2Dmethods Plot organelle assignment data and results.
plot2Ds Draw 2 data sets on one PCA plot
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
prettyGoTermId Convert GO ids to/from terms
pRoloc A unifying bioinformatics framework for spatial proteomics
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"'
setLisacol Manage default colours and point characters
setStockcol Manage default colours and point characters
setStockcolGui 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 Class 'SpatProtVis'
show-method Undocumented/unexported entries
showGOEvidenceCodes GO Evidence Codes
showMrkMat Create a marker vector or matrix.
SpatProtVis Class 'SpatProtVis'
SpatProtVis-class Class 'SpatProtVis'
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