What the Package Does (One Line, Title Case)

add_absolute_proportions_to_tree | Put absolute proportions on tree |

add_data_to_tree_from_table | Put proportions on tree |

add_info_to_tree | Add info to tree |

ARMET-package | The 'ARMET' package. |

ARMET_tc | ARMET-tc main |

ARMET_tc_coreAlg | Core algorithm |

check_if_sd_zero_and_correct | Checks if the standard deviation of a gene is 0 |

check_input | Check the input for anomalies |

create_temp_result_directory | Creates the directory needed for archive |

drop_node_from_tree | Drop a node from the tree |

get_child_and_group_background | Get the right level of the tree and label the leaf |

get_distributions_from_tree | Get information from tree recursively for every node |

get_gene_distributons_recursive | Run ARMET core algorithm recursively on the tree |

get_genes | Get genes from tree |

get_hierarchy | Get cell type hierarchy of a node |

get_ini | Get parameters from ini file if it exists |

get_leave_label | Get any info from the tree |

get_leave_names | Get leaves cell type names |

get_map_foreground_background | Create a map where every leaf is mapped with the right... |

get_node_from_gene | Get nome from gene |

get_node_from_name | Get node from cell type |

get_node_label_level_specfic | Get cell type names from a specific level of the tree |

get_node_label_recursive | Get information from tree recursively for every node |

parse_summary_vector_in_2D | Parse a vector from stan fit object in a 2D matrix |

plot_densities | Plots the densities distributions columnwise of a matrix |

plot_densities_from_melted | Plots the densities from a melted data frame |

prepare_input | Create object for full bayesian model, with the reference... |

quant_norm_to_target | Normalize array to match RNAseq |

rnaseq_norm | Normalize a RNA seq data set using rnaseq_norm.calcNormFactor |

rnaseq_norm.calcNormFactor | Calculate the norm factor with calcNormFactor from limma |

rnaseq_norm.get_cpm | Eliminate lowly tanscribed genes for normalization |

rnaseq_norm.get_low_expressed | Eliminate lowly tanscribed genes for normalization |

rnaseq_norm_ref_mix | Normalize ref to match mix using TMM |

run_coreAlg_though_tree | Run ARMET core algorithm on the tree |

run_coreAlg_though_tree_recursive | Run ARMET core algorithm recursively on the tree |

wrapper_normalize_mix_ref | Wrapper function for all normalization based on the current... |

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