All functions |
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Add annotations to the DAG object |
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Supported methods |
Term-item associations |
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Various types of common ancestors |
Create the ontology_DAG object |
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Create the ontology_DAG object from the GO.db package |
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Create the ontology_DAG object from the igraph object |
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Names of all terms |
Convert to an igraph object |
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Depth and height in the DAG |
Distinct ancestors of a list of terms |
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Enrichment analysis on the number of annotated items |
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Enrichment analysis on offspring terms |
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Enrichment analysis on offspring terms by permutation test |
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Filter the DAG |
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Whether the terms exist in the DAG |
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Distance from all ancestors/to all offspring in the DAG |
Generate a random DAG |
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Reorder the DAG |
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Root or leaves of the DAG |
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A shiny app for the DAG |
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Parent/child/ancestor/offspring terms |
Reduce the DAG to a tree |
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Visualize the DAG |
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Distance on the DAG |
Semantic similarity between two groups of terms |
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Import ontology file to an ontology_DAG object |
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Get or set meta columns on DAG |
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All Papameters of a given method |
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Number of annotated items |
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Number of parent/child/ancestor/offspring/leaf terms |
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Import ontologies already having gene annotations |
The ontology_DAG class |
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Partition the DAG |
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Print the source |
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Randomly sample terms/items |
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Print the ontology_DAG object |
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Global options |
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Create sub-DAGs |
GroupSim_Dice |
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GroupSim_Jaccard |
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GroupSim_Kappa |
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GroupSim_Overlap |
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GroupSim_SimALD |
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GroupSim_SimALN |
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GroupSim_SimCHO |
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GroupSim_SimCOT |
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GroupSim_SimCOU |
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GroupSim_SimDB |
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GroupSim_SimDIC |
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GroupSim_SimGIC |
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GroupSim_SimLP |
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GroupSim_SimNTO |
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GroupSim_SimUB |
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GroupSim_SimUI |
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GroupSim_SimUIC |
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GroupSim_Ye_2005 |
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GroupSim_pairwise_ABM |
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GroupSim_pairwise_BMA |
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GroupSim_pairwise_BMM |
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GroupSim_pairwise_Froehlich_2007 |
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GroupSim_pairwise_HDF |
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GroupSim_pairwise_Joeng_2014 |
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GroupSim_pairwise_MHDF |
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GroupSim_pairwise_VHDF |
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GroupSim_pairwise_avg |
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GroupSim_pairwise_max |
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IC_Meng_2012 |
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IC_Sanchez_2011 |
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IC_Seco_2004 |
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IC_Seddiqui_2010 |
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IC_Wang_2007 |
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IC_Zhang_2006 |
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IC_Zhou_2008 |
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IC_annotation |
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IC_depth |
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IC_offspring |
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IC_universal |
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Sim_AIC_2014 |
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Sim_AlMubaid_2006 |
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Sim_Ancestor |
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Sim_Dice |
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Sim_EISI_2015 |
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Sim_FaITH_2010 |
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Sim_GOGO_2018 |
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Sim_HRSS_2013 |
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Sim_Jaccard |
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Sim_Jiang_1997 |
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Sim_Kappa |
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Sim_Leocock_1998 |
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Sim_Li_2003 |
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Sim_Lin_1998 |
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Sim_Overlap |
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Sim_Pekar_2002 |
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Sim_RSS_2013 |
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Sim_Rada_1989 |
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Sim_Relevance_2006 |
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Sim_Resnik_1999 |
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Sim_Resnik_edge_2005 |
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Sim_SSDD_2013 |
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Sim_Shen_2010 |
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Sim_Shenoy_2012 |
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Sim_SimIC_2010 |
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Sim_Slimani_2006 |
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Sim_Stojanovic_2001 |
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Sim_WP_1994 |
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Sim_Wang_2007 |
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Sim_Wang_edge_2012 |
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Sim_XGraSM_2013 |
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Sim_Zhang_2006 |
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Sim_Zhong_2002 |
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Sim_universal |
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Information content |
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Semantic similarity |