This package implements pattern recognition techniques on quantitiative mass spectrometry data to infer protein sub-cellular localisation.
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| Author | Laurent Gatto and Lisa M. Breckels with contributions from Thomas Burger and Samuel Wieczorek |
| Bioconductor views | Classification Clustering MassSpectrometry Proteomics QualityControl |
| Date of publication | None |
| Maintainer | Laurent Gatto <lg390@cam.ac.uk> |
| License | GPL-2 |
| Version | 1.16.1 |
| URL | https://github.com/lgatto/pRoloc |
| Package repository | View on Bioconductor |
| Installation | Install the latest version of this package by entering the following in R:
|
| Package overview |
| Annotating spatial proteomics data |
Functions | |
|---|---|
| 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 |
| 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 |
| [,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 |
| [[,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 |
| 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:SpatProtVis | Man page |
| class:ThetaRegRes | Man page |
| classWeights | Man page Source code |
| classify | Source code |
| clustDist | Man page Source code |
| clustdists | Source code |
| clusterDistK | 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 |
| diffscore | Source code |
| diffscores | Source code |
| difftorand | Source code |
| dunkley2006params | Man page |
| empPvalues | Man page Source code |
| estimateVariance | Source code |
| exprsToRatios | Man page |
| exprsToRatios,MSnSet-method | Man page |
| exprsToRatios-methods | Man page |
| 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 |
| 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 |
| 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 |
| levelPlot | Man page |
| levelPlot,ClustRegRes-method | Man page |
| levelPlot,GenRegRes-method | Man page |
| levelPlot,QSep-method | Man page |
| loopInTestStep | 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 |
| mahalanobis | Source code |
| makeCol3 | Source code |
| makeF1matrix | Source code |
| makeGoSet | Man page Source code |
| makePartList | Source code |
| make_ans | Source code |
| markerMSnSet | Man page Source code |
| markers | Man page |
| matMarkerMSnSet | Source code |
| matSampleMSnSet | Source code |
| matUnknownMSnSet | Source code |
| meanDist | Source code |
| meanMarkerDist | Source code |
| minClassScore | Man page Source code |
| minMarkers | 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 |
| 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 |
| onAttach | Source code |
| opt | Source code |
| optim.kmeans | Source code |
| orderGoAnnotations | Man page Source code |
| orgQuants | Man page Source code |
| pRoloc | Man page |
| pRoloc-defunct | Man page |
| pRoloc-deprecated | Man page |
| pRoloc-package | Man page |
| pRolocmarkers | Man page Source code |
| pdist | Source code 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,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 |
| plotDist | Man page Source code |
| plotQSep | 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 |
| sbig | Source code |
| 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,GenRegRes-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 |
| 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 |
| testMSnSet | Man page Source code |
| testMarkers | Man page Source code |
| testPerTurbo | Source code |
| testStep | Source code |
| thetas | Man page 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 |
| validpRolocVisMethod | Source code |
| vc.res | Source code |
| vecMarkerMSnSet | Source code |
| vecSampleMSnSet | Source code |
| vecUnknownMSnSet | Source code |
| viction | Source code Source code |
| zerosInBinMSnSet | Man page Source code |
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