Man pages for caravagnalab/lineaGT
lineaGT
| configure_environment | Configure the reticulate environment |
| cov.df.example | Example coverage data |
| estimate_n_pops | Function implemented to estimate the real number of clones in... |
| filter_dataset | Filters the input dataset. |
| fit | Creates an object of class 'mvnmm'. |
| fit_growth_rates | Infer growth rates for each clone and subclone. |
| fit_mutations | Fit the mutations clustering |
| fit_phylogenies | Fit the phylogenetic trees |
| get_covariance_Cholesky | Extract the estimated Cholesky matrices, used to factorise... |
| get_covariance_Sigma | Extract the estimated covariance matrices. |
| get_cov_dataframe | Retrieve the coverage dataframe. |
| get_dimensions | Extract the model dimensions. |
| get_ISs | Get the number of ISs per cluster. |
| get_labels | Extract the observations labels. |
| get_lineages | Extract the data lineages. |
| get_mean | Extract the estimated mean parameters. |
| get_sigma | Extract the estimated variance parameters. |
| get_timepoints | Extract the data timepoints. |
| get_unique_labels | Extract the list of unique observations labels. |
| get_unique_muts_labels | Retrieve the list of unique labels of mutation clusters. |
| get_vaf_dataframe | Retrieve the mutations dataframe. |
| get_weights | Extract the estimated mixing proportions. |
| get_z_probs | Extract the estimated posterior probabilities. |
| have_loaded_env | Check if there is a loaded 'conda' environment. |
| have_python_deps | Check if 'Python' packages are installed in the environment. |
| load_conda_env | Load the input 'conda' environment. |
| plot_differentiation_tree | Visualize the number of subclones on the differentiation tree |
| plot_gradient_norms | Function to plot the gradients norms. |
| plot_growth_rates | Visualize the infered growth rates. |
| plot_growth_regression | Visualize the regression given the infered growth rates. |
| plot_IC | Function to plot the Information Criteria computed during... |
| plot_losses | Function to plot the training losses. |
| plot_marginal | Histogram of the marginal distribution of each dimension |
| plot_mixture_weights | Barplot of the per-cluster mixture weights and number of ISs. |
| plot_mullerplot | Muller plot |
| plot.mvnmm | Mullerplot |
| plot_phylogeny | Clonal evolution trees |
| plot_scatter_density | 2D scatterplot and density |
| plot_vaf | VAF 2D scatterplot |
| plot_vaf_time | VAF over time |
| print.mvnmm | Print method |
| vaf.df.example | Example mutation data |
| which_conda_env | Retrieve the name of the currently loaded environment. |
| x.example | Example mutation data |
