The notebooks in this folder contain code to plot results of running our SAIGE-QTL to map single-cell eQTLs across all 14 cell types from OneK1K, and comparison with performing the same task using TensorQTL.
- ChiSquare SAIGE-QTL vs TensorQTL: Comparison of Chi squared values between SAIGE-QTL and TensorQTL for each cell type.
- CV conditional rounds: Number of eQTLs identified by each of 5 rounds of conditional analysis for each cell type.
- ITGA4 forest plot: Forest plot showing eQTL results (using SAIGE-QTL) for ITGA4 across cell types.
- Scatter n eGenes vs n cells: Scatterplot of number of cells available for each cell type and number of eGenes identified by SAIGE-QTL for the same cell type.
- SAIGE-QTL vs TensorQTL eGenes Venn: For each cell type, plot Venn diagrams to represent the eGene overlap between SAIGE-QTL and TensorQTL.
- SAIGE-QTL vs Matrix eQTL pvs and betas scatter: Scatterplot of negative log p-values and effect sizes (betas) between SAIGE-QTL results and results from the original OneK1K paper using Matrix eQTL.