Function reference • CNHplus

All functions

analyze_TCGA_study(): CNH+ and associated tumor purity, tumor ploidy for samples from TCGA study are found

check_q(): Is the ACN tumor profile q, corresponding to RCN sample profile r, tumor purity, tumor ploidy non-negative in every segment?

find_cnhplus(): For sample RCN profile r finds CNH+ and the associated tumor purity, tumor ploidy

kappa(): Computes value of the objective function kappa for purity, ploidy pair, RCN sample profile r and associated segments width vector w

kappa_q(): Computes value of the objective function kappa for ACN profile q and associated segments width vector w

make_grid(): Makes grid for vectors of purities and ploidies

make_grid_plus(): For given RCN profile r of sample and a grid of purities and ploidies, those pairs for which the tumor ACN profile q fails the non-negativity requirement are removed from the grid

plot_profile(): Plots CN profile

plot_survival(): Plot of survival functions of samples from TCGA study with CNH below or equal to median vs samples with CNH above median

r2q(): Computes Absolute Copy Number (ACN) tumor profile from Relative Copy Number (RCN) sample profile and tumor purity, tumor ploidy

sample_data: Data for TCGA-AJ-A3EJ-01A-11D-A19X-01 sample from TCGA-UCEC study

topk(): Grid of tumor purities, tumor ploidies is sorted by the associated values of kappas (values of the objective function) and top k values (i.e., with the smallest kappa) are returned