SEMgraph (version 1.2.3)

graph2dag: Convert directed graphs to directed acyclic graphs (DAGs)

Description

Remove cycles and bidirected edges from a directed graph.

Usage

graph2dag(graph, data, bap = FALSE, time.limit = Inf, ...)

Value

A DAG as an igraph object.

Arguments

graph

A directed graph as an igraph object.

data

A data matrix with subjects as rows and variables as columns.

bap

If TRUE, a bow-free acyclic path (BAP) is returned (default = FALSE).

time.limit

CPU time for the computation, in seconds (default = Inf).

...

Currently ignored.

Author

Mario Grassi

Details

The conversion is performed firstly by removing bidirected edges and then the data matrix is used to compute edge P-values, through marginal correlation testing (see weightGraph, r-to-z method). When a cycle is detected, the edge with highest P-value is removed, breaking the cycle. If the bap argument is TRUE, a BAP is generated merging the output DAG and the bidirected edges from the input graph.

Examples

dag <- graph2dag(graph = sachs$graph, data = log(sachs$pkc))
old.par <- par(no.readonly = TRUE)
par(mfrow=c(1,2), mar=rep(1, 4))
gplot(sachs$graph, main = "Input graph")
gplot(dag, main = "Output DAG")
par(old.par)