pRoloc
A unifying bioinformatics framework for spatial proteomics

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530
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76
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pRoloc: A unifying bioinformatics framework for spatial proteomics
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API

API for pRoloc
A unifying bioinformatics framework for spatial proteomics

Global functions
.MCMCChain Man page
.MCMCChains Man page
.MCMCParams Man page
.MCMCSummary Man page
.clusterDistK Source code
.diffscore Source code
.isbig Source code
.mahalanobis Source code
.makeCol3 Source code
.make_ans Source code
.meanMarkerDist Source code
.onAttach Source code
.optim.kmeans Source code
.pdist Source code
.plotQSep Source code
.validpRolocVisMethod Source code
.viction Source code
AnnotationParams Man page Man page
AnnotationParams-class Man page
BUG_splitTh Source code
ClustDist Man page
ClustDist-class Man page
ClustDistList Man page Source code
ClustDistList-class Man page
GenRegRes Man page
GenRegRes-class Man page
MAPParams Man page
MAPParams-class Man page
MCMCChain Man page
MCMCChain-class Man page
MCMCChains Man page
MCMCChains-class Man page
MCMCParams-class Man page
MCMCSummary Man page
MCMCSummary-class Man page
MCMCSummary-class. Man page
MLearn,formula,MSnSet,clusteringSchema,missing-method Man page
MLearn,formula,MSnSet,learnerSchema,numeric-method Man page
MLearn,formula,MSnSet,learnerSchema,xvalSpec-method Man page
MLearnMSnSet Man page
MSnSetMLean Man page
MartInstance Man page Source code
MartInstance-class Man page
MartInstanceList Man page Source code
MartInstanceList-class Man page
QSep Man page Source code
QSep-class Man page
SpatProtVis Man page Source code
SpatProtVis-class Man page
ThetaRegRes Man page
ThetaRegRes-class Man page
[,ClustDistList,ANY,ANY,ANY-method Man page
[,ClustDistList,ANY,missing,missing-method Man page
[,MCMCChains,ANY,ANY,ANY-method Man page
[,MCMCParams,ANY,ANY,ANY-method Man page
[,MartInstanceList,ANY,ANY,ANY-method Man page
[,MartInstanceList,ANY,ANY-method Man page
[,MartInstanceList-method Man page
[[,ClustDistList,ANY,ANY-method Man page
[[,ClustDistList,ANY,missing-method Man page
[[,MCMCChains,ANY,ANY-method Man page
[[,MCMCParams,ANY,ANY-method Man page
[[,MartInstanceList,ANY,ANY-method Man page
[[,MartInstanceList-method Man page
addConvexHulls Source code
addGoAnnotations Man page Source code
addLegend Man page Source code
addMarkers Man page Source code
andy2011params Man page
anyUnknown Source code
as.data.frame.MartInstance Man page Source code
as.data.frame.MartInstanceList Man page Source code
bel Source code
chains Man page Source code
checkAttr0 Source code
checkAttrX Source code
checkFeatureNames Source code
checkFeatureNamesOverlap Man page Source code
checkFvarOverlap Man page Source code
checkNumbers Source code
checkSortedFeatureNames Source code
chi2 Man page
chi2,matrix,matrix-method Man page
chi2,matrix,numeric-method Man page
chi2,numeric,matrix-method Man page
chi2,numeric,numeric-method Man page
chi2-methods Man page
chooseAttributesX Source code
class::QSep Man page
class:AnnotationParams Man page
class:ClustDist Man page
class:ClustDistList Man page
class:GenRegRes Man page
class:MAPParams Man page
class:MCMCChain Man page
class:MCMCChains Man page
class:MCMCParams Man page
class:MCMCSummary Man page
class:SpatProtVis Man page
class:ThetaRegRes Man page
classWeights Man page Source code
classify Source code
clustDist Man page Source code
clustdists Source code
col1 Man page Source code
col2 Man page Source code
combineParams Source code
combineThetaRegRes Man page Source code
constructDataSet Source code
controlParameters Source code
createPartitions Source code
data1 Man page Source code
data2 Man page Source code
diffscores Source code
difftorand Source code
dimred Source code
dmvtCpp Source code
dunkley2006params Man page
empPvalues Man page Source code
estimateVariance Source code
f1Count Man page
f1Count,GenRegRes-method Man page
f1Count,ThetaRegRes-method Man page
fDataToUnknown Man page Source code
favourPrimary Man page Source code
filterAttrs Man page Source code
filterBinMSnSet Man page Source code
filterMaxMarkers Man page Source code
filterMinMarkers Man page Source code
filterZeroCols Man page Source code
filterZeroRows Man page Source code
flipGoTermId Man page Source code
getAnnotationParams Man page Source code
getAttributesOfInterest0 Source code
getAttributesOfInterestX Source code
getBestParams Source code
getClusterInfo Source code
getF1Scores Man page
getF1Scores,GenRegRes-method Man page
getF1Scores,ThetaRegRes-method Man page
getFilterList Man page Source code
getFiltersOfInterest Source code
getGOEvidenceCodes Man page Source code
getGOFromFeatures Man page Source code
getGONamespace Source code
getLisacol Man page Source code
getMarkerClasses Man page Source code
getMarkerCols Source code
getMarkerMatClasses Source code
getMarkerVecClasses Source code
getMarkers Man page Source code
getMartInstanceList Man page Source code
getMartTab Man page Source code
getMatMarkers Source code
getNN Source code
getNewClusters Source code
getNormDist Man page Source code
getOldcol Man page Source code
getParams Man page
getParams,ClustRegRes-method Man page
getParams,GenRegRes-method Man page
getParams,ThetaRegRes-method Man page
getPrediction Source code
getPredictions Man page Source code
getRegularisedParams Man page
getRegularisedParams,GenRegRes-method Man page
getRegularizedParams Man page
getRegularizedParams,GenRegRes-method Man page
getSeed Man page
getSeed,GenRegRes-method Man page
getStockcol Man page Source code
getStockpch Man page Source code
getUnknowncol Man page Source code
getUnknownpch Man page Source code
getVecMarkers Source code
getWarnings Man page
getWarnings,GenRegRes-method Man page
geweke_test Man page Source code
gmmOutlier Source code
goIdToTerm Man page Source code
goTermToId Man page Source code
highlightOnPlot Man page Source code
highlightOnPlot3D Man page Source code
isBinary Source code
isMrkMat Man page Source code
isMrkVec Man page Source code
knnClassification Man page Source code
knnOptimisation Man page Source code
knnOptimization Man page
knnPrediction Man page Source code
knnRegularisation Man page Source code
knntlClassification Man page Source code
knntlOptimisation Man page Source code
ksvmClassification Man page Source code
ksvmOptimisation Man page Source code
ksvmOptimization Man page
ksvmPrediction Man page Source code
ksvmRegularisation Man page Source code
lapply,ClustDistList-method Man page
lapply,MartInstanceList,ANY-method Man page
lapply,MartInstanceList-method Man page
learnOneClass Source code
length,ClustDistList-method Man page
length,MCMCChains-method Man page
length,MCMCParams-method Man page
levelPlot Man page
levelPlot,ClustRegRes-method Man page
levelPlot,GenRegRes-method Man page
levelPlot,QSep-method Man page
logPosteriors Man page Source code
lopims Man page Source code
lopims1 Man page Source code
lopims2 Man page Source code
lopims3 Man page Source code
lopims4 Man page Source code
lopims5 Man page Source code
makeF1matrix Source code
makeGoSet Man page Source code
makePartList Source code
markerMSnSet Man page Source code
markers Man page
matMarkerMSnSet Source code
matSampleMSnSet Source code
matUnknownMSnSet Source code
mcmc_burn_chains Man page Source code
mcmc_get_meanComponent Man page Source code
mcmc_get_meanoutliersProb Man page Source code
mcmc_get_outliers Man page Source code
mcmc_plot_probs Source code
mcmc_pool_chains Man page Source code
mcmc_thin_chains Man page Source code
meanDist Source code
minClassScore Man page Source code
minMarkers Man page Source code
mixing_posterior_check Man page Source code
move2Ds Man page Source code
mrkConsProfiles Man page Source code
mrkEncoding Man page Source code
mrkHClust Man page Source code
mrkMatAndVec Man page Source code
mrkMatToVec Man page Source code
mrkVecToMat Man page Source code
nDatasets Man page Source code
names,ClustDistList-method Man page
names,QSep-method Man page
names<-,ClustDistList,ANY-method Man page
names<-,QSep,character-method Man page
nbClassification Man page Source code
nbOptimisation Man page Source code
nbOptimization Man page
nbPrediction Man page Source code
nbRegularisation Man page Source code
nicheMeans2D Man page Source code
nndist Man page
nndist,MSnSet,missing-method Man page
nndist,matrix,matrix-method Man page
nndist,matrix,missing-method Man page
nndist-methods Man page
nndist_matrix Source code
nndist_msnset Source code
nndistx_matrix Source code
nnetClassification Man page Source code
nnetOptimisation Man page Source code
nnetOptimization Man page
nnetPrediction Man page Source code
nnetRegularisation Man page Source code
nologgin Source code
normDist Source code
orderGoAnnotations Man page Source code
orgQuants Man page Source code
pRoloc-defunct Man page
pRoloc-deprecated Man page
pRolocmarkers Man page Source code
pdist Source code
perTurboClassification Man page Source code
perTurboOptimisation Man page Source code
perTurboOptimization Man page
phat Source code
phenoDisco Man page Source code
pl Source code
plot,ClustDist,MSnSet-method Man page
plot,ClustDistList,missing-method Man page
plot,ClustRegRes,missing-method Man page
plot,GenRegRes,missing-method Man page
plot,MCMCParams,character-method Man page
plot,QSep,missing-method Man page
plot,QSep-method Man page
plot,SpatProtVis,missing-method Man page
plot,ThetaRegRes,missing-method Man page
plot2D Man page Source code
plot2Dmethods Man page
plot2Ds Man page Source code
plot3D,MSnSet-method Man page
plotConsProfiles Man page Source code
plotDist Man page Source code
plotDist_fcol Source code
plotEllipse Man page Source code
plotEllipse_old Source code
plotMetropolisHastings Source code
plotThetas Source code
plsdaClassification Man page Source code
plsdaOptimisation Man page Source code
plsdaOptimization Man page
plsdaPrediction Man page Source code
plsdaRegularisation Man page Source code
powerset Source code
predictionPerTurbo Source code
prettyGoTermId Man page Source code
print.plot2Ds Source code
qsep Man page Source code
refNormMeanOfNonNAPepSum Source code
refNormMedOfPepRatio Source code
remap Source code
rfClassification Man page Source code
rfOptimisation Man page Source code
rfOptimization Man page
rfPrediction Man page Source code
rfRegularisation Man page Source code
sampleMSnSet Man page Source code
sapply,ClustDistList-method Man page
sapply,MartInstanceList,ANY-method Man page
sapply,MartInstanceList-method Man page
separateDataSet Source code
setAnnotationParams Man page Source code
setLisacol Man page Source code
setOldcol Man page Source code
setStockcol Man page Source code
setStockpch Man page Source code
setUnknowncol Man page Source code
setUnknownpch Man page Source code
show,AnnotationParams-method Man page
show,ClustDist-method Man page
show,ClustDistList-method Man page
show,ClustRegRes-method Man page
show,ComponentParam-method Man page
show,GenRegRes-method Man page
show,MAPParams-method Man page
show,MCMCChain-method Man page
show,MCMCChains-method Man page
show,MCMCParams-method Man page
show,MartInstance-method Man page
show,QSep-method Man page
show,SpatProtVis-method Man page
show,ThetaRegRes-method Man page
showGOEvidenceCodes Man page Source code
showMrkMat Man page Source code
spatial2D Man page Source code
splitTh Source code
subsetAsDataFrame Source code
subsetMarkers Man page Source code
summariseMatList Source code
summary,QSep-method Man page
svmClassification Man page Source code
svmOptimisation Man page Source code
svmOptimization Man page
svmPrediction Man page Source code
svmRegularisation Man page Source code
tagmMapPredict Man page Source code
tagmMapTrain Man page Source code
tagmMcmcChain Source code
tagmMcmcPredict Man page Source code
tagmMcmcProcess Man page Source code
tagmMcmcTrain Man page Source code
tagmPredict Man page Source code
testMSnSet Man page Source code
testMarkers Man page Source code
testPerTurbo Source code
testStep Source code
thetas Man page Source code
tlopt Source code
tracking Source code
trainingPerTurbo Source code
trainingStep Source code
trainingStepAutoSigma Source code
undocumented Man page
unknownMSnSet Man page Source code
updateobject Source code
vc.res Source code
vecMarkerMSnSet Source code
vecSampleMSnSet Source code
vecUnknownMSnSet Source code
viction Source code
zerosInBinMSnSet Man page Source code
pRoloc documentation built on Nov. 8, 2020, 6:26 p.m.

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