# Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding

## Documentation for package ‘MethScope’ version 1.0.3

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

## Help Pages

confidence_score | Produce confidence score for XGBoost prediction
confidence_score_top95 | Produce confidence score based on top 95 percent for XGBoost prediction
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
Liu2021_MouseBrain_P1000 | Load the Liu et al. mouse brain pretrained model
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 eg.100kb bin widows
PredictCellType | Predict cell type annotation from the trained model
smooth_matrix | Smooth cell by pattern matrix to reduce noise
Zhou2025_HumanAtlas_P1000 | Load the Zhou et al. human atlas pretrained model