Description Usage Arguments Value Examples

A function producing a refitted predictive model for each panel produced by usage of the function pred_first_fit(), by repeatedly applying the function pred_refit_panel().

1 2 3 4 5 6 7 8 9 10 11 12 |

`pred_first` |
(list) A first-fit predictive model as produced by pred_first_fit(). |

`gene_lengths` |
(dataframe) A dataframe of gene lengths (see example_maf_data$gene_lengths for format). |

`model` |
(character) A choice of "T", "OLM" or "Count" specifying how predictions should be made. |

`biomarker` |
(character) If "TMB" or "TIB", automatically defines marker_mut_types, otherwise this will need to be specified separately. |

`marker_mut_types` |
(character) A vector specifying which mutation types groups determine the biomarker in question. |

`training_data` |
(sparse matrix) Training matrix, as produced by get_mutation_tables() (select train, val or test). |

`training_values` |
(dataframe) Training true values, as produced by get_biomarker_tables() (select train, val or test). |

`mutation_vector` |
(numeric) Optional vector specifying the values of the training matrix (training_data$matrix) in vector rather than matrix form. |

`t_s` |
(numeric) Optional vector specifying the frequencies of different mutation types. |

`max_panel_length` |
(numeric) Upper bound for panels to fit refitted models to. Most useful for "OLM" and "Count" model types. |

A list with three elements:

fit, a list including a sparse matrix 'beta' giving prediction weights for each first-fit panel (one panel per column).

panel_genes, a sparse (logical) matrix giving the genes included in prediction for each first-fit panel.

panel_lengths, a vector giving the length of each first-fit panel.

1 2 | ```
example_refit_range <- pred_refit_range(pred_first = example_first_pred_tmb,
gene_lengths = example_maf_data$gene_lengths)
``` |

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