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