netgsa: Network-Based Gene Set Analysis

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Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.

Author
Ali Shojaie and Jing Ma
Date of publication
2016-06-16 18:27:48
Maintainer
Jing Ma <jinma@upenn.edu>
License
GPL (>= 2)
Version
3.0
URLs

View on CRAN

Man pages

bic.netEst.undir
Bayesian information criterion to select the tuning...
edgelist
An example edge list
edgelist2adj
Construct an adjacency matrix from an edge list
netEst.dir
Constrained estimation of directed networks
netEst.undir
Constrained estimation of undirected networks
NetGSA
Network-based Gene Set Analysis
netgsaex2
Toy example for using 'NetGSA' on a two-class test with...
netgsaex3
Toy example for using 'NetGSA' on a three-class test with...
netgsaexDAG
Toy example for using 'NetGSA' on a two-class test with...
netgsa-package
Network-Based Gene Set Analysis
nonedgelist
An example for not-an-edge list

Files in this package

netgsa
netgsa/NAMESPACE
netgsa/data
netgsa/data/netgsaexDAG.rda
netgsa/data/netgsaex2.rda
netgsa/data/netgsaex3.rda
netgsa/data/nonedgelist.rda
netgsa/data/edgelist.rda
netgsa/R
netgsa/R/profile.newton.se.R
netgsa/R/NetGSA.R
netgsa/R/normalizeAdj.R
netgsa/R/zeroInd.R
netgsa/R/glmnet.soft.R
netgsa/R/netgsa.ttest.R
netgsa/R/netgsa.ftest.R
netgsa/R/get.contrast.R
netgsa/R/call.netgsa.R
netgsa/R/edgelist2adj.R
netgsa/R/matTr.R
netgsa/R/newton.R
netgsa/R/netEst.undir.R
netgsa/R/adj2inf.R
netgsa/R/bic.netEst.undir.R
netgsa/R/graphlaplacian.R
netgsa/R/netEst.dir.R
netgsa/R/approxVarEst.R
netgsa/R/netgsa-internal.R
netgsa/MD5
netgsa/DESCRIPTION
netgsa/man
netgsa/man/bic.netEst.undir.Rd
netgsa/man/nonedgelist.Rd
netgsa/man/netgsaexDAG.Rd
netgsa/man/NetGSA.Rd
netgsa/man/edgelist2adj.Rd
netgsa/man/netEst.dir.Rd
netgsa/man/netgsa-package.Rd
netgsa/man/netgsaex2.Rd
netgsa/man/netgsaex3.Rd
netgsa/man/netEst.undir.Rd
netgsa/man/edgelist.Rd