netOmics: netOmics: network-based multi-omics integration and...

In abodein/netOmics: Multi-Omics (time-course) network-based integration and interpretation

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 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.

Network building

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.

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.

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.

combine_layers

Combine 2 (or list of) graphs based on given intersections.

Network exploration

random_walk_restart

This function performs a propagation analysis by random walk with restart in a multi-layered network from specific seeds.

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.

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.

Visualisation

summary_plot_rwr_attributes

#' Based on the results of 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.

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.

Author(s)

Maintainer: Antoine Bodein [e-mail]

See Also

Useful links:

• https://github.com/abodein/netOmics

• Report bugs at https://github.com/abodein/netOmics/issues

abodein/netOmics documentation built on April 16, 2024, 2:59 p.m.