find_edges: find links between nodes

In rmflight/STRINGDatabaseManipulation: Provides Utilities for Working With STRING Data

Description

given a data frame of edges, find nodes within so many edges of initial nodes with option that final set of edges go to known nodes

Usage

find_edges(in_graph, start_nodes, n_hop = 1, end_nodes = NULL,
  drop_same_after_2 = TRUE)

Arguments

in_graph	a graphBAM graph
start_nodes	which nodes to start from
n_hop	how many hops to go out (default is 1)
end_nodes	optional, only keep edges that end at these nodes
drop_same_after_2	should edges that only go to a single other node be dropped? Default is TRUE. See DETAILS for more information.

Details

One frequently encountered case will be a set of nodes that do: N1 –> N2 –> N1 (because the network is assumed to be undirected), where after a single hop from N1 we reach N2, and then a second hop returns to N1. Even in the case where the end_nodes are the same as the start_nodes, this is likely not useful information. So drop_same_after_1 = TRUE will set the results so that these edge paths are not returned and kept in the final graph.

Value

list

Examples

library(STRINGDatabaseManipulation)
library(graph)
set.seed(1234)
link_data <- STRING10_links
link_data <- link_data[sample(nrow(link_data), 10000),]
link_graph <- string_2_graphBAM(link_data)
start_nodes <- sample(nodes(link_graph), 10)
end_nodes <- NULL
n_hop <- 3
find_edges(link_graph, start_nodes, n_hop)

find_edges(link_graph, start_nodes, n_hop, end_nodes, drop_same_after_2 = FALSE)

rmflight/STRINGDatabaseManipulation documentation built on Feb. 7, 2020, 12:26 a.m.