matrinet_graph: Create matrigraph object

In KontioJuho/matrinetR: R package for the Analysis of extracellular matrix network dynamics

Create matrigraph object

Description

Create the initial skeleton of matrigraph object for storing network data.

Usage

matrinet_graph(
  matridata,
  prior_topology,
  add_node_df = NULL,
  add_edge_df = NULL
)

Arguments

matridata	The output from matrinet_data() function or any list of group (cancer) specific data-frames containing node covariates, e.g., gene or protein expression data. Extracted automatically from the dataframe by the column names of prior_topology object.
prior_topology	An adjacency matrix providing a fixed skeleton for the network. The default structure is given by the matrixDB interaction data.
add_node_df	A data-frame for custom node attributes that are common for each group (e.g. protein/gene family).
add_edge_df	A data-frame for custom edge attributes that are common for each group (e.g. gene-gene interaction data source).

Value

Returns a list of group (cancer) specific matrigraph objects, with 1) node_df, 2) edge_df and 3) summary dataframes. Matrigraph object is meant for storing network estimation results and custom node/edge attributes.

Examples

print(c("matrinet_graph(matridata, prior_topology)"))

KontioJuho/matrinetR documentation built on June 19, 2022, 3:56 p.m.