├── .Rhistory ├── .Rproj.user ├── 452674CE │ ├── console06 │ │ └── INDEX001 │ ├── cpp-definition-cache │ ├── pcs │ │ ├── files-pane.pper │ │ ├── source-pane.pper │ │ ├── windowlayoutstate.pper │ │ └── workbench-pane.pper │ ├── rmd-outputs │ └── saved_source_markers └── shared │ └── notebooks │ └── patch-chunk-names ├── .gitignore ├── LICENSE ├── README.Rmd ├── README.log ├── README.md ├── R_package.Rproj ├── SClineager.Rcheck ├── 00_pkg_src │ └── SClineager │ │ ├── DESCRIPTION │ │ ├── NAMESPACE │ │ ├── R │ │ ├── RcppExports.R │ │ ├── SClineager_eda.R │ │ ├── SClineager_fitting.R │ │ └── SClineager_io.R │ │ ├── man │ │ ├── explore_sclineager.Rd │ │ ├── read_sclineager.Rd │ │ ├── run_sclineager.Rd │ │ ├── sclineager_gibbs.Rd │ │ └── sclineager_internal.Rd │ │ └── src │ │ ├── Gibbs.cpp │ │ ├── Gibbs.h │ │ ├── Gibbs.o │ │ ├── Makevars │ │ ├── Makevars.win │ │ ├── RcppExports.cpp │ │ ├── RcppExports.o │ │ ├── SClineager.so │ │ ├── misc.cpp │ │ ├── misc.h │ │ ├── misc.o │ │ └── symbols.rds ├── 00check.log ├── 00install.out ├── Rdlatex.log ├── SClineager-Ex.R ├── SClineager-Ex.Rout ├── SClineager-Ex.pdf ├── SClineager-manual.log ├── SClineager-manual.pdf └── SClineager │ ├── DESCRIPTION │ ├── INDEX │ ├── Meta │ ├── Rd.rds │ ├── features.rds │ ├── hsearch.rds │ ├── links.rds │ ├── nsInfo.rds │ └── package.rds │ ├── NAMESPACE │ ├── R │ ├── SClineager │ ├── SClineager.rdb │ └── SClineager.rdx │ ├── help │ ├── AnIndex │ ├── SClineager.rdb │ ├── SClineager.rdx │ ├── aliases.rds │ └── paths.rds │ ├── html │ ├── 00Index.html │ └── R.css │ └── libs │ ├── SClineager.so │ └── symbols.rds ├── SClineager ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── RcppExports.R │ ├── SClineager_eda.R │ ├── SClineager_fitting.R │ └── SClineager_io.R ├── man │ ├── explore_sclineager.Rd │ ├── read_sclineager.Rd │ ├── run_sclineager.Rd │ ├── sclineager_gibbs.Rd │ └── sclineager_internal.Rd └── src │ ├── Gibbs.cpp │ ├── Gibbs.h │ ├── Gibbs.o │ ├── Makevars │ ├── Makevars.win │ ├── RcppExports.cpp │ ├── RcppExports.o │ ├── SClineager.so │ ├── misc.cpp │ ├── misc.h │ └── misc.o ├── data ├── CTCL.RData ├── coverage.txt ├── germline_mutations_mm10.txt └── toy_data.RData └── fig ├── QBRC.jpg └── toy_VAF.png /.Rhistory: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.Rproj.user/452674CE/console06/INDEX001: -------------------------------------------------------------------------------- 1 | [] -------------------------------------------------------------------------------- /.Rproj.user/452674CE/cpp-definition-cache: -------------------------------------------------------------------------------- 1 | [ 2 | ] -------------------------------------------------------------------------------- /.Rproj.user/452674CE/pcs/files-pane.pper: -------------------------------------------------------------------------------- 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