subgraph_op: Extract PPI subgraph by genes of interest

In AnaGalhoz37/wppi: Weighting protein-protein interactions

Extract PPI subgraph by genes of interest

Description

From the igraph object of a PPI network obtained from OmniPath extracts a subnetwork around the provided genes of interest. The size of the graph is determined by the sub_level parameter, i.e. the maximum number of steps (order) from the genes of interest.

Usage

subgraph_op(graph_op, gene_set, sub_level = 1L)

Arguments

graph_op	Igraph object based on OmniPath PPI interactions from graph_from_op.
gene_set	Character vector of gene symbols. These are the genes of interest, for example known disease specific genes.
sub_level	Integer larger than 0 defining the order of neighborhood (number of steps) from the genes of interest. If not specified, the first-order neighbors are used.

Value

Igraph graph object with PPI network of given genes of interest and their x-order degree neighbors.

Examples

# Subgraphs of first and second order
graph_op <- graph_from_op(wppi_omnipath_data())
genes_interest <-
    c("ERCC8", "AKT3", "NOL3", "GFI1B", "CDC25A", "TPX2", "SHE")
graph_op_1 <- subgraph_op(graph_op, genes_interest, 1)
graph_op_2 <- subgraph_op(graph_op, genes_interest, 2)

AnaGalhoz37/wppi documentation built on Nov. 8, 2022, 7:47 a.m.