netOmics: netOmics: network-based multi-omics integration and...
In abodein/netOmics: Multi-Omics (time-course) network-based integration and interpretation
netOmics R Documentation
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_grnBased 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_databaseFrom 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_correlationCompute 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_layersCombine 2 (or list of) graphs based on given
intersections.
Network exploration
random_walk_restartThis function performs a propagation analysis
by random walk with restart
in a multi-layered network from specific seeds.
rwr_find_seeds_between_attributesFrom 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_typeFrom 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_subnetworkDisplay 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 antoine.bodein.1@ulaval.ca
See Also
Useful links:
abodein/netOmics documentation built on Oct. 20, 2024, 9:25 a.m.
R Package Documentation
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| netOmics | R Documentation |
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_grnBased 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_databaseFrom 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_correlationCompute 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_layersCombine 2 (or list of) graphs based on given intersections.
Network exploration
random_walk_restartThis function performs a propagation analysis by random walk with restart in a multi-layered network from specific seeds.
rwr_find_seeds_between_attributesFrom 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_typeFrom 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_attributeswhich identify the closest k neighbors from a seed, this function returns a barplot of the node types (layers) reached for each seed.plot_rwr_subnetworkDisplay 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 antoine.bodein.1@ulaval.ca
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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