Get GeneMANIA Edges — GetGeneMANIA.edges • PTMsToPathways

This function returns 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).

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")
)

Arguments

gm.results.path: Path to GeneMANIA results text file (used when local = FALSE).
gene.cccn.nodes: A list of nodes that are in the Gene CoCluster Correlation Network derived from common clusters between the three distance metrics (Euclidean, Spearman, and Combined (SED))
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. Only used when local = TRUE. Default retains Pathway and Physical Interactions, matching the filter applied in the original live mode.

Value

Data frame of consisting of the network of interactions from the genes of study

Details

Live mode: To get the GeneMANIA results text file, click on the three lines in the upper right corner of the GeneMANIA side window beside the species. Click "Export Results". The path to this file is the gm.results.path.

Local mode: Download and process the full GeneMANIA Homo sapiens network using the companion script scripts/genemania_hs_download.r, which produces hs_interactions_hugo.tsv.

Examples

# Live mode (original behaviour):
ex.gm.results.path <- system.file("extdata/ex_gm_edgetable.csv", package = "PTMsToPathways")
example.GeneMANIA.edges <- GetGeneMANIA.edges(ex.gm.results.path, ex.gene.cccn.nodes)
#> Warning: file("") only supports open = "w+" and open = "w+b": using the former
#> Error in start_line[1]:(end_line[1] - 1): NA/NaN argument

# Local mode (future-proof, no internet required):
# example.GeneMANIA.edges <- GetGeneMANIA.edges(
#   gm.results.path    = NULL,
#   gene.cccn.nodes    = ex.gene.cccn.nodes,
#   local              = TRUE,
#   genemania.local.path = "hs_interactions_hugo.tsv"
# )

utils::head(example.GeneMANIA.edges)
#> Error: object 'example.GeneMANIA.edges' not found