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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/netOmics-package.R
+\docType{package}
+\name{netOmics}
+\alias{netOmics-package}
+\alias{netOmics}
+\title{netOmics: network-based multi-omics integration and interpretation}
+\description{
+netOmics is a multi-omics networks builder and explorer.
+It uses a combination of network inference algorithms and and knowledge-based
+graphs to build multi-layered networks.
+
+The package can be combined with
+\code{timeOmics} to incorporate time-course expression data and build
+sub-networks from multi-omics kinetic clusters.
+
+Finally, from the generated multi-omics networks, propagation analyses allow
+the identification of missing biological functions (1),
+multi-omics mechanisms (2) and molecules between kinetic clusters (3).
+This helps to resolve complex regulatory mechanisms.
+Here are the main functions.
+}
+\section{Network building}{
+
+\describe{
+\item{\code{get_grn}}{Based on expression matrix, this function build a gene
+gene regulatory network. Additionally, if clustering information is given,
+it builds cluster specific graph.}
+\item{\code{get_interaction_from_database}}{From a database (graph or data.frame
+with interactions between 2 molecules), this function build the induced
+graph based on a list of molecules . Alternatively, the function can
+build a graph with the first degree neighbors.}
+\item{\code{get_interaction_from_correlation}}{Compute correlation between two
+dataframe X and Y (or list of data.frame).
+An incidence graph is returned. A link between two features is produced
+if their correlation (absolute value) is above the threshold.}
+\item{\code{combine_layers}}{Combine 2 (or list of) graphs based on given
+intersections.}
+}
+}
+
+\section{Network exploration}{
+
+\describe{
+\item{\code{random_walk_restart}}{This function performs a propagation analysis
+by random walk with restart
+in a multi-layered network from specific seeds.}
+\item{\code{rwr_find_seeds_between_attributes}}{From rwr results, this function
+returns a subgraph if any vertex shares
+different attributes value.
+In biological context, this might be useful to identify vertex shared between
+clusters or omics types.}
+\item{\code{rwr_find_closest_type}}{From a rwr results, this function returns
+the closest nodes from a seed with
+a given attribute and value.
+In biological context, it might be useful to get the closest Gene Ontology
+annotation nodes from unannotated seeds.}
+}
+}
+
+\section{Visualisation}{
+
+\describe{
+\item{\code{summary_plot_rwr_attributes}}{#' Based on the results of
+\code{\link[netOmics]{rwr_find_seeds_between_attributes}} which identify the
+closest k neighbors from a seed, this function returns a barplot of the node
+types (layers) reached for each seed.}
+\item{\code{plot_rwr_subnetwork}}{Display the subgraph from a RWR results.
+This function colors adds a specific
+color to each node based on their 'type' attribute.
+It also adds a legend including the number of vertices/edges and the number
+of nodes of specific type.
+Additionally, the function can display any igraph object.}
+}
+}
+
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://github.com/abodein/netOmics}
+  \item Report bugs at \url{https://github.com/abodein/netOmics/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Antoine Bodein \email{antoine.bodein.1@ulaval.ca}
+
+}