# Network-Based Gene Set Analysis

## Documentation for package ‘netgsa’ version 4.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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