Network-Based Gene Set Analysis

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Documentation for package ‘netgsa’ version 4.0.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

netgsa-package	Network-Based Gene Set Analysis
bic.netEst.undir	Bayesian information criterion to select the tuning parameters for 'netEst.undir'
breastcancer2012_subset	Breast cancer data from TCGA (2012). This is a 750 gene subset
edgelist	A data frame of edges, each row corresponding to one edge
formatPathways	Format cytoscape nested networks
group	The vector of class indicators
netEst.dir	Constrained estimation of directed networks
netEst.undir	Constrained estimation of undirected networks
NetGSA	Network-based Gene Set Analysis
NetGSAq	"Quick" Network-based Gene Set Analysis
nonedgelist	A data frame of nonedges, each row corresponding to one negative edge
obtainClusters	Estimate optimal gene clustering structure
obtainEdgeList	Obtain edgelist from graphite databases. To be used within prepareAdjMat
pathways	A list of KEGG pathways
pathways_mat	Matrix with pathway indicators
plot.NetGSA	Generates NetGSA plots
prepareAdjMat	Construct adjacency matrices from graphite databases and/or user provided network information
stackDatabases	Combine edges from databases into a data.table
x	Data matrix p by n
zoomPathway	Zoom in on pathway in igraph