├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── AllClasses.R ├── AllGenerics.R ├── datasets.R ├── estimatecc.R ├── find_dmrs.R ├── helper_functions.R └── methods.R ├── README.md ├── data ├── FlowSorted.Blood.450k.sub.RData ├── offMethRegions.RData └── onMethRegions.RData ├── inst ├── CITATION ├── NEWS └── objectCreation.R ├── man ├── FlowSorted.Blood.450k.sub.Rd ├── cell_counts.Rd ├── dot-WFun.Rd ├── dot-extract_raw_data.Rd ├── dot-find_dmrs.Rd ├── dot-initializeMLEs.Rd ├── dot-initialize_theta.Rd ├── dot-methylcc_engine.Rd ├── dot-methylcc_estep.Rd ├── dot-methylcc_mstep.Rd ├── dot-pick_target_positions.Rd ├── dot-preprocess_estimatecc.Rd ├── dot-splitit.Rd ├── estimatecc-class.Rd ├── estimatecc.Rd ├── offMethRegions.Rd └── onMethRegions.Rd ├── tests ├── testthat.R └── testthat │ └── test-estimatecc.R └── vignettes └── methylCC.Rmd /.gitignore: -------------------------------------------------------------------------------- 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