DiffusionProfiles

S7 class for the diffusion profiles of Ruiz et al.: one constrained personalised PageRank per seed over a heterogeneous graph. The seed is a source; every other node of a sink type absorbs the walker. With type weights, the walker at node i first picks a neighbouring node type proportional to its weight, then a neighbour of that type.

Usage

DiffusionProfiles(
  graph_dt,
  node_dt,
  sink_types,
  type_weights = NULL,
  directed = FALSE
)

Arguments

graph_dt

data.table. The edge table. Needs the columns "from" and "to", optionally "weight" (non-negative). Every endpoint needs to be in node_dt$id.

node_dt

data.table. The node table with the columns "id" and "type".

sink_types

Character vector. Node types that absorb the walker, e.g. c("drug", "disease"). Can be empty.

type_weights

Optional named numeric vector. Positive weight per node type; needs to cover every type in node_dt. NULL gives the plain (edge-weighted) random walk.

directed

Boolean. Treat the graph as directed. Defaults to FALSE.

Value

An initialised DiffusionProfiles object.

Properties

graph_dt

data.table. The edge table with from, to and optionally weight.

node_dt

data.table. The node table with id and type.

sink_types

Character vector. Node types that act as sinks.

type_weights

Named numeric vector of weights per node type, or NULL for the plain random walk.

profiles

Numeric matrix of nodes x seeds. NULL until generate_profiles() is called.

params

Named list of the parameters used.

References

Ruiz, Zitnik and Leskovec, Identification of disease treatment mechanisms through the multiscale interactome, Nat Commun 2021.