# Network-Based Gene Set Analysis

## Documentation for package ‘netgsa’ version 3.1.0

- 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 | Breast cancer data from TCGA (2012).
edgelist | A data frame of edges, each row corresponding to one edge
g | A directed acyclic graph corresponding to the Adrenergic signaling in cardiomyocytes pathway from KEGG
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
nonedgelist | A data frame of nonedges, each row corresponding to one negative edge
pathways | A list of KEGG pathways
prepareAdjacencyMatrix | Construct adjacency matrices from existing databases or user provided network information
preparePathways | Prepare pathway dataset needed by NetGSA
x | Data matrix p by n