MRPC (version 2.0.0)

DendroModuleGraph : Visualization of Nodes by Dendrogram with Modules and Inferred Graph

Description

Clustering dendrogram of nodes with dissimilarity based on topological overlap, together with assigned module colors and graphical visualization.

Usage

DendroModuleGraph (Adj_directed,minModuleSize,GV)

Arguments

Adj_directed

Adjacency matrix from directed graph

minModuleSize

Minimum module size.

GV

Number of SNPs/indels/CNV/eQTL in the input data matrix. For example, If the data has one SNPs/indels/CNV/eQTL (first column), then GV = 1, if 2 SNPs/indels/CNV/eQTL (1st and 2nd Column), then GV = 2, and so on.

Value

A list containing the graph objects as follows:

• obj: An object of class "graph" of the estimated graph.

• GroupMods: A list of modules containing the number of nodes in each module.

• Adjmatrixdirected: The adjacency matrix of the directed graph used to extract directed edges along with their nodes.

See Also

MRPC for estimating a DAG using the Mendelian Randomization (MR) based PC (MRPC) algorithm; ModiSkeleton for estimating a skeleton using the modified skeleton function; EdgeOrientation for orientation rules used to determine the edges in MRPC; SimulatedData for simulated data generating function.

Examples

# NOT RUN {
# Adjacency matrix from directed example graph
Adj_directed <- as(ExampleMRPC$complex$cont$withGV$graph,
                   "matrix")

# Plot of the graph
DendroModuleGraph(Adj_directed,
                  minModuleSize = 5,
                  GV = 14)
# }