Man pages for MethScope
Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding
| confidence_score | Produce confidence score for XGBoost prediction |
| confidence_score_top95 | Produce confidence score based on top 95 percent for XGBoost... |
| filter_cell | Filter final prediction to reduce noise |
| GenerateInput | Generate pattern level data for cell type annotation |
| GenerateReference | Generate reference pattern labels (no default writing) |
| imputeRowMean | Impute missing value for 100K window matrix |
| Input_training | Train XGBoost model to predict cell type |
| nnls_deconv | Estimate cell type relative proportion |
| PlotConfusion | Generate confusion table for the final prediction |
| PlotF1 | Generate F1 score barplot for each class |
| PlotUMAP | Generate UMAP for the final prediction based on cell patterns |
| PlotUMAP_fixedwindow | Generate UMAP for the final prediction based on fixed window... |
| PredictCellType | Predict cell type annotation from the trained model |
| smooth_matrix | Smooth cell by pattern matrix to reduce noise |
