Deduplicate edges

Collapses duplicate edges into one. The constrained PageRank keeps parallel edges, so a pair listed twice (e.g. the same gene pair from two interaction sources, or A-B plus B-A in an undirected graph) gets twice the transition weight. Run this before DiffusionProfiles() unless that is what you want.

Usage

dedup_edges(
  graph_dt,
  node_dt = NULL,
  directed = FALSE,
  weight_agg = c("max", "sum", "mean"),
  .verbose = TRUE
)

Arguments

graph_dt

data.table. The edge table with "from", "to" and optionally "weight" (non-negative).

node_dt

Optional data.table with the columns "id" and "type". If supplied, the removed duplicates are reported per node-type pair.

directed

Boolean. If FALSE, A-B and B-A are the same edge. Defaults to FALSE.

weight_agg

String. How to combine the weights of duplicates. One of c("max", "sum", "mean"). Ignored without a "weight" column. Defaults to "max", matching the deduplication in node2vec().

.verbose

Boolean. Controls verbosity. Defaults to TRUE.

Value

A data.table with the columns "from", "to" and, if present in the input, "weight". All other columns are dropped. For undirected graphs each edge is stored once with from <= to (lexicographically). Endpoints are returned as character.