Network Analysis for Omics Data
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Documentation for package ‘MetaNet’ version 0.1.2
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A C D E F G I L M N O P R S T V Z
-- A --
| anno_edge | Use dataframe to annotate edges of an igraph |
| anno_node | Use data.frame to annotate vertexes of metanet |
| anno_vertex | Use data.frame to annotate vertexes of metanet |
| arc_count | Edgelist |
| arc_taxonomy | Edgelist |
| as.ggig | Transfer an igraph object to a ggig |
| as.metanet | Update a metanet object or transform igraph object to metanet object |
| as_arc | Layout as a arc |
| as_circle_tree | Layout as a circle_tree |
| as_line | Layout as a line |
| as_polyarc | Layout as a polyarc |
| as_polycircle | Layout as a polycircle |
| as_polygon | Layout as a polygon |
-- C --
| cal_sim | Calculate similarity for one t(otutab) |
| check_tabs | Check tables and extract common samples |
| clean_igraph | Clean a igraph object |
| Cohesion | Cohesion calculation |
| combine_n_module | Filter some modules as others |
| compare_rand | Net_pars of many random network |
| co_net | MetaNet networks |
| co_net2 | MetaNet networks |
| co_net_rmt | MetaNet networks |
| c_net_annotate | Annotate a metanet |
| c_net_build | Construct a metanet from a corr object |
| c_net_cal | Calculate correlation for one or two t(otutab), or distance for one t(otutab). |
| c_net_calculate | Calculate correlation for one or two t(otutab), or distance for one t(otutab). |
| c_net_filter | Filter a network according to some attributes |
| c_net_from_edgelist | Construct a network from edge_list dataframe |
| c_net_index | Calculate all topological indexes of a network |
| c_net_lay | Layout coordinates |
| c_net_layout | Layout coordinates |
| c_net_module | Detect the modules |
| c_net_plot | Plot a metanet |
| c_net_save | Save network file |
| c_net_set | Set basic attributes from totu table |
| c_net_stability | Evaluate the stability of a network |
| c_net_union | Union two networks |
| c_net_update | Update a metanet object or transform igraph object to metanet object |
-- D --
| df2net_tree | Transform a dataframe to a network edgelist. |
-- E --
| extract_sub_net | Extract sub-network from the whole network |
-- F --
| fast_cor | Fast correlation calculation |
| filter_n_module | Filter some modules as others |
| fit_power | Fit power-law distribution for an igraph |
-- G --
| get_community | Get community |
| get_e | Get edge information |
| get_group_skeleton | Get skeleton network according to a group |
| get_module | Get module |
| get_module_eigen | Get module_eigen |
| get_n | Get network information |
| get_v | Get vertex information |
| g_layout | Layout with group |
| g_layout_nice | Layout with group |
| g_layout_polyarc | Layout with group as a polygon |
| g_layout_polycircle | Layout with group as a polygon |
| g_layout_polygon | Layout with group as a polygon |
-- I --
| input_corr | Import corr from .csv file |
| input_gephi | Input a graphml file exported by Gephi |
| is.metanet | Is this object a metanet object? |
| is_metanet | Is this object a metanet object? |
-- L --
| links_stat | Link summary of the network |
-- M --
| metab | MetaNet networks abundance |
| metab_g | MetaNet networks metadata |
| micro | MetaNet networks abundance |
| micro_g | MetaNet networks metadata |
| module_detect | Detect the modules |
| module_eigen | Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor). |
| module_expression | Calculate the eigenvalue of each module and correlation of nodes and eigenvalue (node_eigen_cor). |
| module_net | Generate a n-modules network |
| multi1 | MetaNet networks |
| multi_net_build | Multi-omics network build |
-- N --
| nc | Calculate natural_connectivity |
| netD3plot | plot use networkD3 |
| net_par | Calculate all topological indexes of a network |
-- O --
| olympic_rings_net | Plot olympic rings using network |
-- P --
| p.adjust.table | p.adjust apply on a correlation table (matrix or data.frame) |
| plot.cohesion | Cohesion calculation |
| plot.ggig | Plot a ggig |
| plot.metanet | Plot a metanet |
| plot.rmt_res | Plot a rmt_res |
| plot.robust | Plot robust |
| plot.robustness | Plot robustness |
| plot.vulnerability | Plot vulnerability |
| plot_module_tree | Filter some modules as others |
| print.cohesion | Print method for 'cohesion' objects |
| print.coors | Print method for 'coors' objects |
| print.corr | Print method for 'corr' objects |
| print.ggig | Print method for 'ggig' objects |
| print.metanet | Print method for 'metanet' objects |
| print.robust | Print method for 'robust' objects |
| print.robustness | Print method for 'robustness' objects |
| print.vulnerability | Print method for 'vulnerability' objects |
-- R --
| rand_net | Degree distribution comparison with random network |
| rand_net_par | Net_pars of many random network |
| rmt | Get RMT threshold for a correlation matrix |
| RMT_threshold | Get RMT threshold for a correlation matrix |
| robustness | Evaluate the stability of a network |
| robust_test | Evaluate the stability of a network |
-- S --
| show_MetaNet_logo | Show MetaNet logo |
| skeleton_plot | Get skeleton network according to a group |
| smallworldness | Calculate small-world coefficient |
| summary_module | Summary module index |
| summ_2col | Summaries two columns information |
-- T --
| to_module_net | Transformation a network to a module network |
| transc | MetaNet networks abundance |
| transc_g | MetaNet networks metadata |
| twocol_edgelist | Quick build a metanet from two columns table |
-- V --
| venn_net | Venn network |
| vulnerability | Evaluate the stability of a network |
-- Z --
| zp_analyse | Zi-Pi calculate |
| zp_plot | Zi-Pi calculate |