Man pages for caravagnalab/mobster
MOBSTER - Model-based tumour subclonal deconvolution
| bootstrapped_statistics | Compute boostrap statistics from a bootstrap run. |
| cancer_genes_dnds | List of cancer genes to compute dnds values. |
| choose_clusters | Filter MOBSTER output clusters. |
| Clusters | Return the data with the hard clustering assigments. |
| Clusters_denovo | Assign new observations to the clusters inside a MOBSTER fit. |
| ddbpmm | Density function for MOBSTER. |
| dnds | Run a dN/dS analysis on MOBSTER clusters. |
| evolutionary_parameters | Extract evolutionary parameters from a MOBSTER fit |
| fit_example | Example MOBSTER fit. |
| get_clone_trees | Return clone trees from the fit. |
| load_vcf | Load data from a VCF file |
| LU4_lung_sample | MOBSTER fit for the LU4 lung sample. |
| LUFF76_lung_sample | MOBSTER fit for the LUFF76 lung sample. |
| mobster_bootstrap | Bootstrap a MOBSTER fit. |
| mobster_fit | Fit a model with MOBSTER. |
| plot_bootstrap_Beta | Plot the boostrapped tail parameters. |
| plot_bootstrap_coclustering | Plot the boostrapped co-clustering probability. |
| plot_bootstrap_mixing_proportions | Plot the boostrapped mixing proportions |
| plot_bootstrap_model_frequency | Plot the boostrapped model frequency |
| plot_bootstrap_tail | Plot the boostrapped tail parameters. |
| plot.dbpmm | Plot a MOBSTER fit. |
| plot_entropy | Plot the entropy of a MOBSTER mixture. |
| plot_fit_scores | Plot the scores for model selection. |
| plot_gofit | Plot the goodness of fit. |
| plot_init | Plot the initial density of a fit. |
| plot_latent_variables | Plot the latent variables of the mixture. |
| plot_mixing_proportions | Plot the mixing proportions of the mixture. |
| plot_model_selection | Plot summary for model selection. |
| plot_NLL | Plot the NLL trace. |
| print.dbpmm | Summaries for an object of class "dbpmm" is like a print. |
| random_dataset | Generate a random MOBSTER model and data. |
| rdbpmm | Generate a random sample from a MOBSTER model. |
| summary.dbpmm | Summary for an object of class "dbpmm" is a print. |
| to_string | Return a tabular representation of a model. |
