Deconvolution of Bulk RNA-Seq Data Based on Deep Learning
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Documentation for package ‘digitalDLSorteR’ version 1.0.1
Help Pages
-- B --
| barErrorPlot | Generate bar error plots |
| barPlotCellTypes | Bar plot of deconvoluted cell type proportions in bulk RNA-Seq samples |
| barPlotCellTypes-method | Bar plot of deconvoluted cell type proportions in bulk RNA-Seq samples |
| blandAltmanLehPlot | Generate Bland-Altman agreement plots between predicted and expected cell type proportions from test data results |
| bulk.simul | Get and set 'bulk.simul' slot in a 'DigitalDLSorter' object |
| bulk.simul-method | Get and set 'bulk.simul' slot in a 'DigitalDLSorter' object |
| bulk.simul<- | Get and set 'bulk.simul' slot in a 'DigitalDLSorter' object |
| bulk.simul<--method | Get and set 'bulk.simul' slot in a 'DigitalDLSorter' object |
-- C --
| calculateEvalMetrics | Calculate evaluation metrics for bulk RNA-Seq samples from test data |
| cell.names | Get and set 'cell.names' slot in a 'ProbMatrixCellTypes' object |
| cell.names-method | Get and set 'cell.names' slot in a 'ProbMatrixCellTypes' object |
| cell.names<- | Get and set 'cell.names' slot in a 'ProbMatrixCellTypes' object |
| cell.names<--method | Get and set 'cell.names' slot in a 'ProbMatrixCellTypes' object |
| cell.types | Get and set 'cell.types' slot in a 'DigitalDLSorterDNN' object |
| cell.types-method | Get and set 'cell.types' slot in a 'DigitalDLSorterDNN' object |
| cell.types<- | Get and set 'cell.types' slot in a 'DigitalDLSorterDNN' object |
| cell.types<--method | Get and set 'cell.types' slot in a 'DigitalDLSorterDNN' object |
| corrExpPredPlot | Generate correlation plots between predicted and expected cell type proportions from test data |
| createDDLSobject | Create a 'DigitalDLSorter' object from single-cell RNA-seq and bulk RNA-seq data |
-- D --
| deconv.data | Get and set 'deconv.data' slot in a 'DigitalDLSorter' object |
| deconv.data-method | Get and set 'deconv.data' slot in a 'DigitalDLSorter' object |
| deconv.data<- | Get and set 'deconv.data' slot in a 'DigitalDLSorter' object |
| deconv.data<--method | Get and set 'deconv.data' slot in a 'DigitalDLSorter' object |
| deconv.results | Get and set 'deconv.results' slot in a 'DigitalDLSorter' object |
| deconv.results-method | Get and set 'deconv.results' slot in a 'DigitalDLSorter' object |
| deconv.results<- | Get and set 'deconv.results' slot in a 'DigitalDLSorter' object |
| deconv.results<--method | Get and set 'deconv.results' slot in a 'DigitalDLSorter' object |
| deconvDDLSObj | Deconvolute bulk gene expression samples (bulk RNA-Seq) |
| deconvDigitalDLSorter | Deconvolute bulk RNA-Seq samples using a pre-trained DigitalDLSorter model |
| DigitalDLSorter | The DigitalDLSorter Class |
| digitalDLSorteR | digitalDLSorteR: an R package to deconvolute bulk RNA-Seq samples using single-cell RNA-Seq data and Deep Learning |
| DigitalDLSorter-class | The DigitalDLSorter Class |
| DigitalDLSorterDNN | The DigitalDLSorterDNN Class |
| DigitalDLSorterDNN-class | The DigitalDLSorterDNN Class |
| distErrorPlot | Generate box plots or violin plots to show how the errors are distributed |
-- E --
| estimateZinbwaveParams | Estimate the parameters of the ZINB-WaVE model to simulate new single-cell RNA-Seq expression profiles |
-- F --
| features | Get and set 'features' slot in a 'DigitalDLSorterDNN' object |
| features-method | Get and set 'features' slot in a 'DigitalDLSorterDNN' object |
| features<- | Get and set 'features' slot in a 'DigitalDLSorterDNN' object |
| features<--method | Get and set 'features' slot in a 'DigitalDLSorterDNN' object |
-- G --
| generateBulkCellMatrix | Generate training and test cell composition matrices |
| getProbMatrix | Getter function for the cell composition matrix |
-- I --
| installTFpython | Install Python dependencies for digitalDLSorteR |
-- L --
| listToDDLS | Transform DigitalDLSorter-like list into an actual DigitalDLSorterDNN object |
| listToDDLSDNN | Transform DigitalDLSorterDNN-like list into an actual DigitalDLSorterDNN object |
| loadDeconvData | Load data to be deconvoluted into a DigitalDLSorter object |
| loadDeconvData-method | Load data to be deconvoluted into a DigitalDLSorter object |
| loadTrainedModelFromH5 | Load from an HDF5 file a trained Deep Neural Network model into a 'DigitalDLSorter' object |
-- M --
| method | Get and set 'method' slot in a 'ProbMatrixCellTypes' object |
| method-method | Get and set 'method' slot in a 'ProbMatrixCellTypes' object |
| method<- | Get and set 'method' slot in a 'ProbMatrixCellTypes' object |
| method<--method | Get and set 'method' slot in a 'ProbMatrixCellTypes' object |
| model | Get and set 'model' slot in a 'DigitalDLSorterDNN' object |
| model-method | Get and set 'model' slot in a 'DigitalDLSorterDNN' object |
| model<- | Get and set 'model' slot in a 'DigitalDLSorterDNN' object |
| model<--method | Get and set 'model' slot in a 'DigitalDLSorterDNN' object |
-- P --
| plots | Get and set 'plots' slot in a 'ProbMatrixCellTypes' object |
| plots-method | Get and set 'plots' slot in a 'ProbMatrixCellTypes' object |
| plots<- | Get and set 'plots' slot in a 'ProbMatrixCellTypes' object |
| plots<--method | Get and set 'plots' slot in a 'ProbMatrixCellTypes' object |
| plotTrainingHistory | Plot training history of a trained DigitalDLSorter Deep Neural Network model |
| preparingToSave | Prepare 'DigitalDLSorter' object to be saved as an RDA file |
| prob.cell.types | Get and set 'prob.cell.types' slot in a 'DigitalDLSorter' object |
| prob.cell.types-method | Get and set 'prob.cell.types' slot in a 'DigitalDLSorter' object |
| prob.cell.types<- | Get and set 'prob.cell.types' slot in a 'DigitalDLSorter' object |
| prob.cell.types<--method | Get and set 'prob.cell.types' slot in a 'DigitalDLSorter' object |
| prob.matrix | Get and set 'prob.matrix' slot in a 'ProbMatrixCellTypes' object |
| prob.matrix-method | Get and set 'prob.matrix' slot in a 'ProbMatrixCellTypes' object |
| prob.matrix<- | Get and set 'prob.matrix' slot in a 'ProbMatrixCellTypes' object |
| prob.matrix<--method | Get and set 'prob.matrix' slot in a 'ProbMatrixCellTypes' object |
| ProbMatrixCellTypes | The Class ProbMatrixCellTypes |
| ProbMatrixCellTypes-class | The Class ProbMatrixCellTypes |
| project | Get and set 'project' slot in a 'DigitalDLSorter' object |
| project-method | Get and set 'project' slot in a 'DigitalDLSorter' object |
| project<- | Get and set 'project' slot in a 'DigitalDLSorter' object |
| project<--method | Get and set 'project' slot in a 'DigitalDLSorter' object |
-- S --
| saveRDS | Save 'DigitalDLSorter' objects as RDS files |
| saveRDS-method | Save 'DigitalDLSorter' objects as RDS files |
| saveTrainedModelAsH5 | Save a trained 'DigitalDLSorter' Deep Neural Network model to disk as an HDF5 file |
| set | Get and set 'set' slot in a 'ProbMatrixCellTypes' object |
| set-method | Get and set 'set' slot in a 'ProbMatrixCellTypes' object |
| set.list | Get and set 'set.list' slot in a 'ProbMatrixCellTypes' object |
| set.list-method | Get and set 'set.list' slot in a 'ProbMatrixCellTypes' object |
| set.list<- | Get and set 'set.list' slot in a 'ProbMatrixCellTypes' object |
| set.list<--method | Get and set 'set.list' slot in a 'ProbMatrixCellTypes' object |
| set<- | Get and set 'set' slot in a 'ProbMatrixCellTypes' object |
| set<--method | Get and set 'set' slot in a 'ProbMatrixCellTypes' object |
| showProbPlot | Show distribution plots of the cell proportions generated by 'generateBulkCellMatrix' |
| simBulkProfiles | Simulate training and test pseudo-bulk RNA-Seq profiles |
| simSCProfiles | Simulate new single-cell RNA-Seq expression profiles using the ZINB-WaVE model parameters |
| single.cell.real | Get and set 'single.cell.real' slot in a 'DigitalDLSorter' object |
| single.cell.real-method | Get and set 'single.cell.real' slot in a 'DigitalDLSorter' object |
| single.cell.real<- | Get and set 'single.cell.real' slot in a 'DigitalDLSorter' object |
| single.cell.real<--method | Get and set 'single.cell.real' slot in a 'DigitalDLSorter' object |
| single.cell.simul | Get and set 'single.cell.simul' slot in a 'DigitalDLSorter' object |
| single.cell.simul-method | Get and set 'single.cell.simul' slot in a 'DigitalDLSorter' object |
| single.cell.simul<- | Get and set 'single.cell.simul' slot in a 'DigitalDLSorter' object |
| single.cell.simul<--method | Get and set 'single.cell.simul' slot in a 'DigitalDLSorter' object |
-- T --
| test.deconv.metrics | Get and set 'test.deconv.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.deconv.metrics-method | Get and set 'test.deconv.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.deconv.metrics<- | Get and set 'test.deconv.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.deconv.metrics<--method | Get and set 'test.deconv.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.metrics | Get and set 'test.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.metrics-method | Get and set 'test.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.metrics<- | Get and set 'test.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.metrics<--method | Get and set 'test.metrics' slot in a 'DigitalDLSorterDNN' object |
| test.pred | Get and set 'test.pred' slot in a 'DigitalDLSorterDNN' object |
| test.pred-method | Get and set 'test.pred' slot in a 'DigitalDLSorterDNN' object |
| test.pred<- | Get and set 'test.pred' slot in a 'DigitalDLSorterDNN' object |
| test.pred<--method | Get and set 'test.pred' slot in a 'DigitalDLSorterDNN' object |
| trainDDLSModel | Train Deep Neural Network model |
| trained.model | Get and set 'trained.model' slot in a 'DigitalDLSorter' object |
| trained.model-method | Get and set 'trained.model' slot in a 'DigitalDLSorter' object |
| trained.model<- | Get and set 'trained.model' slot in a 'DigitalDLSorter' object |
| trained.model<--method | Get and set 'trained.model' slot in a 'DigitalDLSorter' object |
| training.history | Get and set 'training.history' slot in a 'DigitalDLSorterDNN' object |
| training.history-method | Get and set 'training.history' slot in a 'DigitalDLSorterDNN' object |
| training.history<- | Get and set 'training.history' slot in a 'DigitalDLSorterDNN' object |
| training.history<--method | Get and set 'training.history' slot in a 'DigitalDLSorterDNN' object |
-- Z --
| zinb.params | Get and set 'zinb.params' slot in a 'DigitalDLSorter' object |
| zinb.params-method | Get and set 'zinb.params' slot in a 'DigitalDLSorter' object |
| zinb.params<- | Get and set 'zinb.params' slot in a 'DigitalDLSorter' object |
| zinb.params<--method | Get and set 'zinb.params' slot in a 'DigitalDLSorter' object |
| ZinbParametersModel | The Class ZinbParametersModel |
| ZinbParametersModel-class | The Class ZinbParametersModel |
| zinbwave.model | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object |
| zinbwave.model-method | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object |
| zinbwave.model<- | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object |
| zinbwave.model<--method | Get and set 'zinbwave.model' slot in a 'ZinbParametersModel' object |