# Deconvolution of Bulk RNA-Seq Data Based on Deep Learning

## Documentation for package ‘digitalDLSorteR’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D E F G I L M P S T Z

## -- 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