Network Analysis for Omics Data

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Documentation for package ‘MetaNet’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

anno_edge	Use dataframe to annotate edges of an igraph
anno_node	Use data.frame to annotate vertexes of an igraph
anno_vertex	Use data.frame to annotate vertexes of an igraph
arc_count	Edgelist
arc_taxonomy	Edgelist
as.metanet	Update a metanet
as_arc	Layout as a arc
as_line	Layout as a line
as_polyarc	Layout as a poly_arc
as_polygon	Layout as a polygon
check_tabs	Check tables
Cohesion	Cohesion calculate
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_build	Construct a network from correlation table
c_net_cal	Calculate spearman correlation for one or two 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 indexes of a network
c_net_lay	Layout coordinates
c_net_plot	Plot a metanet
c_net_save	Save network file
c_net_set	Set basic attributes from totu table
c_net_update	Update a metanet
df2net_tree	Transfer a dataframe to a network edgelist.
extract_sub_net	Extract sub-network from the whole network
filter_n_module	Filter some modules as others
fit_power	Fit power-law distribution for an igraph
f_cor	Fast correlation
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_lay	Layout with group
g_lay_nice	Layout with group
g_lay_polyarc	Layout with group as a polygon
g_lay_polygon	Layout with group as a polygon
input_corr	Import corr from .csv file
input_gephi	Input a graphml file exported by Gephi
is.metanet	Is this object an metanet graph?
is_metanet	Is this object an metanet graph?
links_stat	Link summary of the network
metab	MetaNet networks abundance
metab_g	MetaNet networks metadata
micro	MetaNet networks abundance
micro_g	MetaNet networks metadata
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).
modu_dect	Detect the modules
modu_net	Generate a n-modules network
multi1	MetaNet networks
multi_net_build	Multi-omics network build
my_network_tree	My Network plot
nc	Calculate natural_connectivity
netD3plot	plot use networkD3
net_par	Calculate all indexes of a network
olympic_rings_net	Plot olympic rings using network
p.adjust.table	p.adjust apply on a correlation table (matrix or data.frame)
par_sim	Calculate distance for otutab
plot.cohesion	Cohesion calculate
plot.ggig	Plot a ggig
plot.metanet	Plot a metanet
plot.rmt_res	Plot a rmt_res
plot.robust	Robust_test for a network
plot.robustness	Robustness after remove 50%% nodes or some hubs, need the metanet contains "cor" attribute.
plot.vulnerability	Vulnerability
plot_module_tree	Filter some modules as others
print.coors	Print method for 'coors' objects
print.metanet	Print method for 'metanet' objects
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	Robustness after remove 50%% nodes or some hubs, need the metanet contains "cor" attribute.
robust_test	Robust_test for a network
show_MetaNet_logo	Show MetaNet logo
skeleton_plot	Get skeleton network according to a group
smallworldness	Calculate small-world coefficient
summ_2col	Summaries two columns information
summ_module	Summary module index
to.ggig	Transfer an igraph object to a ggig
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
venn_net	Venn network
vulnerability	Vulnerability
zp_analyse	Zi-Pi calculate
zp_plot	Zi-Pi calculate