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\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}

}