Function reference
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GenerateInput() - Generate pattern level data for cell type annotation
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GenerateReference() - Generate reference pattern file
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Input_training() - Train XGBoost model to predict cell type
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PlotConfusion() - Generate confusion table for the final prediction
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PlotF1() - Generate F1 score barplot for each class
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PlotUMAP() - Generate UMAP for the final prediction based on cell patterns
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PlotUMAP_fixedwindow() - Generate UMAP for the final prediction based on fixed window eg.100kb bin widows
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PredictCellType() - Predict cell type annotation from the trained model
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confidence_score() - Produce confidence score for XGBoost prediction
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confidence_score_top95() - Produce confidence score based on top 95 percent for XGBoost prediction
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filter_cell() - Filter final prediction to reduce noise
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imputeRowMean() - Impute missing value for 100K window matrix
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nnls_deconv() - Estimate cell type relative proportion
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smooth_matrix() - Smooth cell by pattern matrix to reduce noise