Sparse Graph-based Analysis

alias_arbiter | Assign consistant ID to variable given various alias IDs from... |

append_by_enrich | Add vertices to a list based on p-value cutoff / enrichment |

append_vertices_to_lists | Append vertices in a list to vertex lists depending on... |

comp_bipartite_prob | Approximate the probability of interactions between two... |

comp_edgeset_prob | Compute edgeset probability. |

comp_enrichment | Calculate the enrichment within an ordered list of verticies. |

comp_lambda | Compute the number of expected connections between a set of... |

comp_lambda_bipartite | Compute the number of expected connections between two sets... |

comp_outside_vertex_prob | Approximate the probability of a vertex not within a list... |

comp_pij | Compute the probability of vertex i connecting to vertex j. |

comp_sparse_prob | Compute probability for sparse graph edges. |

comp_vertex_prob | Approximate the probability of each vertex within a list... |

construct_graph | Construct graph from data.frame |

count_edges | Count edges within a graph or edges between two... |

map_names | Match gene names within data to vertex identifiers with a... |

plot_bipartite | Plot bipartite graph using ggnet2 |

plot_cluster | Plot cluster with probablistic coloring of the nodes with... |

plot_clusters | Plot graph with a list of vertex lists using ggnet2 |

plot_enrichment_analysis | Plot enrichment analysis of ordered verticies. |

plot_subgraph | Plot subgraph using ggnet2 |

prune_by_enrich | Prune vertices from vertex list based on p-value cutoff /... |

sparseness | Test graph for sparseness |

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