Description Usage Arguments Value

execute bayesNMF for signature deconvolution

1 2 3 | ```
run_bayesNMF(mat, tumor.type = "tumor.type", max_k = 10, n_runs = 10,
iter_per_run = 1e+05, tol = 1e-07, a0 = 10, phi = 1, prior = "L1KL",
hyper = FALSE)
``` |

`mat` |
(matrix) N*M matrix of ints with N mutation frequencies for each of M samples |

`max_k` |
(int) max hypothesized number of signatures to look for. default: 10 |

`n_runs` |
(int) number of times to run optimization code. default: 10 |

`iter_per_run` |
(int) number of iter for each run. default: 100000 |

`tol` |
(float) tolerance used to assess convergence |

`a0` |
(int) value of hyperparameter 'a'. default: 10 |

`phi` |
(int) value of hyperparameter 'phi'. default: 1 (appropriate for l1-loss with exponential prior) |

`prior` |
(chr) either L1KL (expoential priors) or L2KL (half-normal priors). default: L1KL |

`hyper` |
(logical) if TRUE, reduce the effect of hyper-mutant samples in the signature discovery. default: FALSE |

`tumor_name` |
(chr) name of tumor, used for plotting headers, etc. default: 'tumor.type' |

list of signatures, where each signature is a named list containing plots & data

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