Network-Based Gene Set Analysis


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Documentation for package ‘netgsa’ version 3.1.0

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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