dnet (version 1.0.0)

dDAGlevel: Function to define/calculate the level of nodes in a direct acyclic graph (DAG)

Description

dDAGlevel is supposed to calculate the level of nodes, given a direct acyclic graph (DAG; an ontology). The input is a graph of "igraph" or "graphNET" object, and the definition of the node level. The return can be the level for each node or the nodes for each level.

Usage

dDAGlevel(g, level.mode = c("longest_path", "shortest_path"),
return.mode = c("node2level", "level2node"))

Arguments

g

an object of class "igraph" or "graphNEL"

level.mode

the mode of how to define the level of nodes in DAG. It can be "longest_path" for defining the node level as the length of the longest path from the node to the root, and "shortest_paths" for defining the node level as the length of the shortest path from

return.mode

the mode of how to return the node level information. It can be "node2level" for returning a named vector (i.e. the level for each node), and "level2node" for returning a named list (i.e. nodes for each level)

Value

• When "return.mode" is "node2level", it returns a named vector: for each named node (i.e. Term ID), it stores its level When "return.mode" is "level2node", it returns a named list: for each named level, it contains the names (i.e. Term ID) of nodes belonging to this level

See Also

dDAGroot, dDAGreverse

Examples

# 1) load GO Molelular Function as igraph object
load(url("http://dnet.r-forge.r-project.org/data/Obo/ig.GOMF.RData"))
g <- ig.GOMF

# 2) randomly select vertices as the query nodes
nodes_query <- sample(V(g),5)$name

# 3) obtain the complete subgraph induced
subg <- dDAGinduce(g, nodes_query)

# 4) calculate the node levels
# 4a) definition based on the longest path
dDAGlevel(subg, level.mode="longest_path")
# 4b) definition based on the shortest path
dDAGlevel(subg, level.mode="shortest_path")
# 4b) definition based on the longest path, and return nodes for each level
dDAGlevel(subg, level.mode="longest_path", return.mode="level2node")