Network Analysis and Causal Inference Through Structural Equation Modeling

---

Documentation for package ‘SEMgraph’ version 1.1.1

• DESCRIPTION file.

Help Pages

activeModule	Active module identification
alsData	Amyotrophic Lateral Sclerosis (ALS) dataset
ancestors	Node ancestry utilities
ancestry	Node ancestry utilities
clusterGraph	Topological graph clustering
clusterScore	Module scoring
colorGraph	Vertex and edge graph coloring on the base of fitting
corr2graph	Correlation matrix to graph
cplot	Subgraph mapping
descendants	Node ancestry utilities
extractClusters	Cluster extraction utility
gplot	Graph plotting with renderGraph
graph2dag	Convert directed graphs to directed acyclic graphs (DAGs)
graph2dagitty	Graph conversion from igraph to dagitty
graph2lavaan	Graph to lavaan model
kegg	KEGG interactome
kegg.pathways	KEGG pathways
lavaan2graph	lavaan model to graph
mergeNodes	Graph nodes merging by a user-defined membership attribute
modelSearch	Optimal model search strategies
orientEdges	Assign edge orientation of an undirected graph
pairwiseMatrix	Pairwise plotting of multivariate data
parents	Node ancestry utilities
pathFinder	Perturbed path search utility
properties	Graph properties summary and graph decomposition
resizeGraph	Interactome-assisted graph re-seizing
sachs	Sachs multiparameter flow cytometry data and consensus model
SEMace	Compute the Average Causal Effect (ACE) for a given source-sink pair
SEMbap	Bow-free covariance search and data de-correlation
SEMdag	Estimate the optimal DAG from an input graph
SEMdci	SEM-based differential connectivity inference (DCI)
SEMgsa	SEM-based gene set analysis (GSA)
SEMpath	Search for directed or shortest paths between pairs of source-sink nodes
SEMrun	Fit a graph as a Structural Equation Model (SEM)
Shipley.test	Missing edge testing implied by a graph with Shipley's basis-set
siblings	Node ancestry utilities
summary.GGM	GGM model summary
summary.RICF	RICF model summary
weightGraph	Graph weighting methods