get_stringdb_bc_011: Retrieving of information from the STRING database

In InfOmics/LErNet: LErNet: characterization of lncRNAs via context-aware network expansion and enrichment analysis

Description

Retrieves the PPI network form the STRING database via the STRINGdb. STRINGdb often only associates a primary product to a gene, thus other products are not reported. The function also returns the proteins associated to each gene within the STRING database.

Usage

get_stringdb_bc_011(stringdb_tax = 9606, stringdb_thr = 900, mart)

Arguments

stringdb_tax	taxa of the species
stringdb_thr	threshold to be applied to the score on the edges of the PPI
mart	a biomaRt object for mapping proteins to producer genes (Ensembl IDs).

Value

a list

ppi_network

a two columns data.frame representing the PPI network by listing its edges.

ensp_to_ensg

a two columns data.frame reporting for each protein the corresponding gene (Ensembl IDs)

Examples

library(biomaRt)
stringdb_tax = 9606
stringdb_thr = 900
mart = useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
ret <- LErNet::get_stringdb_bc_011( stringdb_tax = stringdb_tax, stringdb_thr = stringdb_thr, mart = mart)
ppi_network <- ret[["ppi_network"]]
ensp_to_ensg <- ret[["ensp_to_ensg"]]

InfOmics/LErNet documentation built on April 10, 2021, 4:49 p.m.