getHumanPPIfromSTRINGdb: Retrieve human protein-protein interaction network from...

In vittoriofortino84/COPS: Clustering algorithms for Omics-driven Patient Stratification

Retrieve human protein-protein interaction network from STRINGdb.

Description

Utility function to extract a gene subnetwork from STRINGdb including only the seed genes and their interactions.

Usage

getHumanPPIfromSTRINGdb(
  gene_ids = NULL,
  cutoff = 700,
  directed = FALSE,
  version = "11",
  gene_id_mart_column = "hgnc_symbol"
)

Arguments

gene_ids	a character vector indicating target genes to include.
cutoff	a numeric value indicating the cutoff for the edge scores.
directed	a boolean value indicating the type of grpah to be generated.
version	a character value specifying STRINGdb version to query from
gene_id_mart_column	column name in biomaRt to translate STRING_ids to

Value

an igraph object.

vittoriofortino84/COPS documentation built on Jan. 28, 2025, 3:16 p.m.