Man pages for pRoloc
A unifying bioinformatics framework for spatial proteomics

addGoAnnotationsAdd GO annotations
addLegendAdds a legend
addMarkersAdds markers to the data
AnnotationParams-classClass '"AnnotationParams"'
checkFeatureNamesOverlapCheck feature names overlap
checkFvarOverlapCompare a feature variable overlap
chi2-methodsThe PCP 'chi square' method
classWeightsCalculate class weights
clustDistPairwise Distance Computation for Protein Information Sets
ClustDist-classClass '"ClustDist"'
ClustDistList-classStoring multiple ClustDist instances
defunctpRoloc Deprecated and Defunct
empPvaluesEstimate empirical p-values for Chi^2 protein correlations.
exprsToRatios-methodsCalculate all ratio pairs
fDataToUnknownUpdate a feature variable
filterBinMSnSetFilter a binary MSnSet
filterMaxMarkersRemoves class/annotation information from a matrix of...
filterMinMarkersRemoves class/annotation information from a matrix of...
filterZeroColsRemove 0 columns/rows
GenRegRes-classClass '"GenRegRes"' and '"ThetaRegRes"'
getGOFromFeaturesRetrieve GO terms for feature names
getMarkerClassesReturns the organelle classes in an 'MSnSet'
getMarkersGet the organelle markers in an 'MSnSet'
getNormDistExtract Distances from a '"ClustDistList"' object
getPredictionsReturns the predictions in an 'MSnSet'
getStockcolManage default colours and point characters
goIdToTermConvert GO ids to/from terms
highlightOnPlotHighlight features of interest on a spatial proteomics plot
knnClassificationknn classification
knnOptimisationknn parameter optimisation
knntlClassificationknn transfer learning classification
knntlOptimisationtheta parameter optimisation
ksvmClassificationksvm classification
ksvmOptimisationksvm parameter optimisation
lopimsA complete LOPIMS pipeline
makeGoSetCreates a GO feature 'MSnSet'
markerMSnSetExtract marker/unknown subsets
markersCreate a marker vector or matrix.
MartInstance-classClass '"MartInstance"'
minMarkersCreates a reduced marker variable
MLearn-methodsThe 'MLearn' interface for machine learning
move2DsDisplays a spatial proteomics animation
mrkConsProfilesMarker consensus profiles
mrkHClustDraw a dendrogram of subcellular clusters
nbClassificationnb classification
nbOptimisationnb paramter optimisation
nndist-methodsNearest neighbour distances
nnetClassificationnnet classification
nnetOptimisationnnet parameter optimisation
orderGoAnnotationsOrders annotation information
orgQuantsReturns organelle-specific quantile scores
perTurboClassificationperTurbo classification
perTurboOptimisationPerTurbo parameter optimisation
phenoDiscoRuns the 'phenoDisco' algorithm.
plot2DPlot organelle assignment data and results.
plot2DsDraw 2 data sets on one PCA plot
plotDistPlots the distribution of features across fractions
plsdaClassificationplsda classification
plsdaOptimisationplsda parameter optimisation
pRolocmarkersOrganelle markers
QSep-classQuantify resolution of a spatial proteomics experiment
rfClassificationrf classification
rfOptimisationsvm parameter optimisation
sampleMSnSetExtract a stratified sample of an 'MSnSet'
showGOEvidenceCodesGO Evidence Codes
SpatProtVis-classClass 'SpatProtVis'
subsetMarkersSubsets markers
svmClassificationsvm classification
svmOptimisationsvm parameter optimisation
testMarkersTests marker class sizes
testMSnSetCreate a stratified 'test' 'MSnSet'
thetasDraw matrix of thetas to test
undocumentedUndocumented/unexported entries
zerosInBinMSnSetCompute the number of non-zero values in each marker classes
pRoloc documentation built on May 24, 2018, 6:01 p.m.