Get GeneMANIA Edges — GetGeneMANIA.edges • PTMsToPathways

Return a filtered GeneMANIA edge list, either by parsing a GeneMANIA Cytoscape export file (original behaviour) or by reading a pre-downloaded full Homo sapiens network (local mode). Optionally standardizes the node list using a precomputed symbol map.

Usage

GetGeneMANIA.edges(
  gm.results.path,
  gene.cccn.nodes,
  local = FALSE,
  genemania.local.path = "hs_interactions_hugo.tsv",
  gm.interaction.types = c("Pathway", "Physical Interactions"),
  symbol.map = NULL
)

Arguments

gm.results.path: Path to GeneMANIA results text file (used when local = FALSE).
gene.cccn.nodes: Character vector of CCCN node symbols.
local: Logical. If TRUE, reads from a pre-downloaded local file instead of a Cytoscape export. Default is FALSE.
genemania.local.path: Path to the pre-processed local GeneMANIA file (hs_interactions_hugo.tsv produced by scripts/genemania_hs_download.r). Only used when local = TRUE. Default is "hs_interactions_hugo.tsv".
gm.interaction.types: Character vector of interaction group names to retain. Default retains Pathway and Physical Interactions.
symbol.map: Optional data frame produced by StandardizeGeneSymbols(). If supplied, gene.cccn.nodes will be converted to standard_symbol before filtering.

Value

Data frame with columns: source, target, interaction, Weight

Examples

# sym.map <- StandardizeGeneSymbols(ex.gene.cccn.nodes)
# gm.edges <- GetGeneMANIA.edges(
#   gm.results.path = ex.gm.results.path,
#   gene.cccn.nodes = ex.gene.cccn.nodes,
#   symbol.map = sym.map
# )