Man pages for pRoloc
A unifying bioinformatics framework for spatial proteomics
| addGoAnnotations | Add GO annotations |
| addLegend | Adds a legend |
| addMarkers | Adds markers to the data |
| AnnotationParams-class | Class '"AnnotationParams"' |
| checkFeatureNamesOverlap | Check feature names overlap |
| checkFvarOverlap | Compare a feature variable overlap |
| chi2-methods | The PCP 'chi square' method |
| classWeights | Calculate class weights |
| clustDist | Pairwise Distance Computation for Protein Information Sets |
| ClustDist-class | Class '"ClustDist"' |
| ClustDistList-class | Storing multiple ClustDist instances |
| defunct | pRoloc Deprecated and Defunct |
| empPvalues | Estimate empirical p-values for Chi^2 protein correlations. |
| fDataToUnknown | Update a feature variable |
| filterBinMSnSet | Filter a binary MSnSet |
| filterMaxMarkers | Removes class/annotation information from a matrix of... |
| filterMinMarkers | Removes class/annotation information from a matrix of... |
| filterZeroCols | Remove 0 columns/rows |
| GenRegRes-class | Class '"GenRegRes"' and '"ThetaRegRes"' |
| getGOFromFeatures | Retrieve GO terms for feature names |
| getMarkerClasses | Returns the organelle classes in an 'MSnSet' |
| getMarkers | Get the organelle markers in an 'MSnSet' |
| getNormDist | Extract Distances from a '"ClustDistList"' object |
| getPredictions | Returns the predictions in an 'MSnSet' |
| getStockcol | Manage default colours and point characters |
| goIdToTerm | Convert GO ids to/from terms |
| highlightOnPlot | Highlight features of interest on a spatial proteomics plot |
| knnClassification | knn classification |
| knnOptimisation | knn parameter optimisation |
| knntlClassification | knn transfer learning classification |
| knntlOptimisation | theta parameter optimisation |
| ksvmClassification | ksvm classification |
| ksvmOptimisation | ksvm parameter optimisation |
| lopims | A complete LOPIMS pipeline |
| makeGoSet | Creates a GO feature 'MSnSet' |
| markerMSnSet | Extract marker/unknown subsets |
| markers | Create a marker vector or matrix. |
| MartInstance-class | Class '"MartInstance"' |
| mcmc-helpers | Number of outlier at each iteration of MCMC |
| MCMCParams | Instrastructure to store and process MCMC results |
| minMarkers | Creates a reduced marker variable |
| mixing_posterior_check | Model calibration plots |
| MLearn-methods | The 'MLearn' interface for machine learning |
| move2Ds | Displays a spatial proteomics animation |
| mrkConsProfiles | Marker consensus profiles |
| mrkHClust | Draw a dendrogram of subcellular clusters |
| nbClassification | nb classification |
| nbOptimisation | nb paramter optimisation |
| nicheMeans2D | Uncertainty plot organelle means |
| nndist-methods | Nearest neighbour distances |
| nnetClassification | nnet classification |
| nnetOptimisation | nnet parameter optimisation |
| orderGoAnnotations | Orders annotation information |
| orgQuants | Returns organelle-specific quantile scores |
| perTurboClassification | perTurbo classification |
| perTurboOptimisation | PerTurbo parameter optimisation |
| phenoDisco | Runs the 'phenoDisco' algorithm. |
| plot2D | Plot organelle assignment data and results. |
| plot2Ds | Draw 2 data sets on one PCA plot |
| plotConsProfiles | Plot marker consenses profiles. |
| plotDist | Plots the distribution of features across fractions |
| plotEllipse | A function to plot probabiltiy ellipses on marker PCA plots... |
| plsdaClassification | plsda classification |
| plsdaOptimisation | plsda parameter optimisation |
| pRolocmarkers | Organelle markers |
| QSep-class | Quantify resolution of a spatial proteomics experiment |
| rfClassification | rf classification |
| rfOptimisation | svm parameter optimisation |
| sampleMSnSet | Extract a stratified sample of an 'MSnSet' |
| showGOEvidenceCodes | GO Evidence Codes |
| spatial2D | Uncertainty plot in localisation probabilities |
| SpatProtVis-class | Class 'SpatProtVis' |
| subsetMarkers | Subsets markers |
| svmClassification | svm classification |
| svmOptimisation | svm parameter optimisation |
| tagm-map | The 'logPosteriors' function can be used to extract the... |
| tagm-mcmc | Localisation of proteins using the TAGM MCMC method |
| testMarkers | Tests marker class sizes |
| testMSnSet | Create a stratified 'test' 'MSnSet' |
| thetas | Draw matrix of thetas to test |
| undocumented | Undocumented/unexported entries |
| zerosInBinMSnSet | Compute the number of non-zero values in each marker classes |
