Signature Multivariate Analysis

assignment | Assigns a boolean based on a threshold on the likelihood or... |

calc_llh | Calculates likelihood of the genome with respect to the... |

cosine | calculates cosine similarity between the spectrum and a set... |

decompose | Decomposes the mutational spectrum of a genome in terms of... |

lite_df | produces a data.frame with fewer columns for easier use |

make_matrix | Converts somatic mutation call files in a directory either in... |

match_to_catalog | Calculates the compatibility of a list of genomes to an input... |

plot_detailed | Generates a detailed plot per sample |

plot_summary | Generates summary plot |

plot_tribase_dist | plots the 96 dimensional mutational spectrum |

predict_mva | This function uses the trained MVA, in particular gradient... |

run | Runs SigMA: (1) calculates likelihood, cosine similarity,... |

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