Description Usage Arguments Value Examples

HIPPO's hierarchical clustering

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`sce` |
SingleCellExperiment object |

`K` |
maximum number of clusters |

`feature_method` |
string, either "zero-inflation" or "deviance" |

`clustering_method` |
string, one of "kmeans", "Seurat", and "SC3" |

`z_threshold` |
numeric > 0 as a z-value threshold for selecting the features |

`deviance_threshold` |
numeric > 0 as a deviance threshold for selecting the features when method is "deviance |

`outlier_proportion` |
numeric between 0 and 1, a cut-off so that when the proportion of important features reach this number, the clustering terminates |

`km_num_embeds` |
number of cell embeddings to use in dimension reduction |

`km_nstart` |
number of tries for k-means for reliability |

`km_iter.max` |
number of maximum iterations for kmeans |

`sc3_n_cores` |
number of cores to use if your method is "SC3" |

`verbose` |
if set to TRUE, shows progress of the algorithm |

a list of clustering result for each level of k=1, 2, ... K.

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