expand_seeds_bc_011: Expansion of the seed network

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

Description

Expands with connectors the network formed by seed proteins, that are the producs fo the genes int he genomic context, by the expasion algorithm. Connectors are neighbors of selected proteins in the input PPI network.

Usage

expand_seeds_bc_011(
  genomic_context,
  ppi_network,
  ensp_to_ensg,
  strict_proteins,
  strict_connectors = TRUE
)

Arguments

genomic_context	a two column data.fram produced by get_genomic_context
ppi_network	a two column data.frame representing PPI network edges (see also get_stringdb )
ensp_to_ensg	a two column data.frame for mapping proteins to their producer genes (see also get_stringdb )
strict_proteins	a list of proteins
strict_connectors	if TRUE connectors can onyl be choosen from the strict_proteins list

Value

a list

network_components

a list of connected components of the resultant expanded network. Each compoent is a list of proteins.

network_seeds

list of seed proteins that have succefully been mapped to the PPI network.

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