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 |