├── .gitignore ├── Copyright ├── DESCRIPTION ├── NAMESPACE ├── R ├── CNA.MCMC.R ├── annotateGenes.hg20.R ├── annotateGenes.mm10.R ├── baseline.GMM.R ├── baseline.norm.cl.R ├── baseline.synthetic.R ├── convert.all.bins.hg20.R ├── copykat.R ├── exp.rawdata.R └── heatmap.3.R ├── README.md ├── copykat.Rproj ├── data-raw ├── .DS_Store └── DATASET.R ├── data ├── .DS_Store ├── exp.rawdata.rda └── sysdata.rda ├── man ├── .DS_Store ├── CNA.MCMC.Rd ├── annotateGenes.hg20.Rd ├── annotateGenes.mm10.Rd ├── baseline.GMM.Rd ├── baseline.norm.cl.Rd ├── convert.all.bins.hg20.Rd ├── copykat.Rd ├── exp.rawdata.Rd └── heatmap.3.Rd ├── test_output ├── test_copykat_CNA_results.txt ├── test_copykat_clustering_results.rda ├── test_copykat_heatmap.jpeg └── test_copykat_prediction.txt └── vignettes ├── .DS_Store ├── .gitignore ├── copycat-vignettes.Rmd └── copycat-vignettes.pdf /.gitignore: -------------------------------------------------------------------------------- 1 | inst/doc 2 | .Rproj.user 3 | 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