Man pages for cozygene/CellTypeSpecificMethylationAnalysis
Evaluation of Cell Type Specific Methylation Analysis
| blood.ref.333cpgs | Methylation reference for cell types in blood |
| celldmc | Run CellDMC method |
| compare_cell_fraction_estimates | Compares cell fraction estimates from EpiDISH and TCA under... |
| compare_runtimes | Compare method runtimes across various input sizes |
| compare_vars_mle | Compares sigma and mu esimtation of TCA with or without... |
| epic_qc | Preprocessing for BBC dataset with ENmix |
| koestler | Koestler Methylation Dataset |
| parametric_simulations | Replicate parametric simulations for power analyses |
| plot_cors | Generates plot with ggplot2 |
| plot_results | Plot performance metrics for BBC and Koestler datasets |
| plot_runtimes | Plots runtime summary dataframe |
| prep_bbc_data | Downloads and processes raw BBC methylation data |
| prep_smoking_data | Download and organize Liu et al. and Hannum et al. Data |
| refit_w_comparison | Replicate cell type fraction analysis of Koestler et al. and... |
| run_smoking_analysis | Smoking analysis of methylation data |
| runtime_comparison | Compare runtimes of CellDMC and TCA (GMM and MLE modes) |
| smoking_analysis | Replicate smoking analysis of Liu et al. and Hannum et al.... |
| summarize_res | Summarizes result dataframe for ggplot2 barplots |
| tca.gmm | Run fast TCA method |
| tca.gmm.reg | Run fast TCA method with tcareg |
| tca.mle | Run original TCA method |
| var_mle_gmm_comparison | Compare parameter estimation of TCA in MLE versus GMM Mode |
