Package index • TorchDecon

Main Workflow

High-level functions for complete deconvolution workflow

RunTorchDecon(): Run Complete TorchDecon Workflow

QuickPredict(): Quick Prediction with Pre-trained Model

Data Simulation

Generate training data from single-cell RNA-seq reference

SimulateBulk(): Simulate Bulk RNA-seq Data from Single-Cell Data

MergeSimulations(): Merge Simulations

ExportSimulation(): Export Simulation to Files

SimulationToDataFrame(): Convert Simulation to Data Frame

Data Processing

Preprocess expression data for model training and prediction

ProcessTrainingData(): Process Training Data for TorchDecon

ProcessPredictionData(): Process Prediction Data

ApplyScaling(): Apply Scaling to New Data

Model Creation & Training

Create, configure, and train deep neural network models

CreateTorchDecon(): Create TorchDecon Model

CreateTorchDeconEnsemble(): Create TorchDecon Ensemble

TrainModel(): Train TorchDecon Model

GetTrainingHistory(): Get Training History

Prediction & Persistence

Make predictions and save/load trained models

PredictFractions(): Predict Cell Type Fractions

SaveModel(): Save TorchDecon Model

LoadModel(): Load TorchDecon Model

Evaluation & Metrics

Evaluate deconvolution performance with multiple metrics

EvaluateDeconvolution(): Evaluate Deconvolution Results

EvaluatePredictions(): Evaluate Predictions

CalculateRMSE(): Calculate RMSE

CalculateMAE(): Calculate MAE

CalculateMRE(): Calculate MRE

CalculateCorrelation(): Calculate Correlation

CalculateAccuracy(): Calculate Accuracy

Visualization

Plotting functions for training and evaluation

PlotTrainingHistory(): Plot Training History

PlotEvaluation(): Plot Evaluation Results

Utilities

Helper functions for Seurat integration

ExtractSeuratData(): Extract Count Matrix from Seurat Object

ExtractCellTypes(): Extract Cell Type Labels from Seurat Object

GenerateExampleData(): Generate Example Data

seurat-utils: Seurat Compatibility Utilities

S3 Methods

Print and summary methods for TorchDecon objects

print(<TorchDeconModel>): Print Method for TorchDeconModel

print(<TorchDeconEnsemble>): Print Method for TorchDeconEnsemble

print(<TorchDeconSimulation>): Print Method for TorchDeconSimulation

print(<TorchDeconProcessed>): Print Method for TorchDeconProcessed

print(<TorchDeconEvaluation>): Print Method for TorchDeconEvaluation

summary(<TorchDeconModel>): Summary Method for TorchDeconModel

summary(<TorchDeconEvaluation>): Summary Method for TorchDeconEvaluation